EMBOSS: emowse

| ## EMBOSS: emowse

# Program emowse

## Function

Protein identification by mass spectrometry

## Description

Peptide mass information can provide a 'fingerprint' signature sufficiently discriminating to allow for the unique and rapid identification of unknown sample proteins, independent of other analytical methods such as protein sequence analysis. Practical experience has shown that sample proteins can be uniquely identified using as few as 3-4 experimentally determined peptide masses when screened against a fragment database derived from over 50,000 proteins.

Given a one-per-line file of molecular weights cut by enzymes/reagents, emowse will search a protein database for matches with the mass spectrometry data.

One of eight cutting enzymes/reagents can be specified and an optional whole sequence molecular weight.

Determination of molecular weight has always been an important aspect of the characterization of biological molecules. Protein molecular weight data, historically obtained by SDS gel electrophoresis or gel permeation chromatography, has been used establish purity, detect post-translational modification (such as phosphorylation or glycosylation) and aid identification. Until just over a decade ago, mass spectrometric techniques were typically limited to relatively small biomolecules, as proteins and nucleic acids were too large and fragile to withstand the harsh physical processes required to induce ionization. This began to change with the development of 'soft' ionization methods such as fast atom bombardment (FAB)[1], electrospray ionisation (ESI) [2,3] and matrix-assisted laser desorption ionisation (MALDI)[4], which can effect the efficient transition of large macromolecules from solution or solid crystalline state into intact, naked molecular ions in the gas phase. As an added bonus to the protein chemist, sample handling requirements are minimal and the amounts required for MS analysis are in the same range, or less, than existing analytical methods.

As well as providing accurate mass information for intact proteins, such techniques have been routinely used to produce accurate peptide molecular weight 'fingerprint' maps following digestion of known proteins with specific proteases. Such maps have been used to confirm protein sequences (allowing the detection of errors of translation, mutation or insertion), characterise post-translational modifications or processing events and assign disulphide bonds [5,6].

Less well appreciated, however, is the extent to which such peptide mass information can provide a 'fingerprint' signature sufficiently discriminating to allow for the unique and rapid identification of unknown sample proteins, independent of other analytical methods such as protein sequence analysis.

Practical experience has shown that sample proteins can be uniquely identified using as few as 3- 4 experimentally determined peptide masses when screened against a fragment database derived from over 50,000 proteins. Experimental errors of a few Daltons are tolerated by the scoring algorithms, permitting the use of inexpensive time-of-flight mass spectrometers. As with other types of physical data, such as amino acid composition or linear sequence, peptide masses can clearly provide a set of determinants sufficiently unique to identify or match unknown sample proteins. Peptide mass fingerprints can prove as discriminating as linear peptide sequence, but can be obtained in a fraction of the time using less material. In many cases, this allows for a rapid identification of a sample protein before committing to protein sequence analysis. Fragment masses also provide structural information, at the protein level, fully complementary to large-scale DNA sequencing or mapping projects [7,8,9].

For each entry in the specified set of sequences to search, emowse derives both whole sequence molecular weight and calculated peptide molecular weights for complete digests using the range of cleavage reagents and rules detailed in Table 1. Cleavage is disallowed if the target residue is followed by proline (except for CNBr or Asp N). Glu C (S. aureus V8 protease) cleavages are also inhibited if the adjacent residue is glutamic acid. Peptide mass calculations are based entirely on the linear sequence and use the average isotopic masses of amide-bonded amino acid residues (IUPAC 1987 relative atomic masses). To allow for N-terminal hydrogen and C-terminal hydroxyl the final calculated molecular weight of a peptide of N residues is given by the equation:

            N
            __
            \
            /  Residue mass + 18.0153
            --
            n=1

Molecular weights are rounded to the nearest integer value before being used. Cysteine residues are calculated as the free thiol, anticipating that samples are reduced prior to mass analysis. CNBr fragments are calculated as the homoserine lactone form. Information relating to post- translational modification (phosphorylation, glycosylation etc.) is not incorporated into calculation of peptide masses.

### Table 1: Cleavage reagents modelled by emowse.

    Reagent no.     Reagent                 Cleavage rule

            1       Trypsin                 C-term to K/R
            2       Lys-C                   C-term to K
            3       Arg-C                   C-term to R
            4       Asp-N                   N-term to D
            5       V8-bicarb               C-term to E
            6       V8-phosph               C-term to E/D
            7       Chymotrypsin            C-term to F/W/Y/L/M
            8       CNBr                    C-term to M

Current versions of emowse also incorporate calculated peptide Mw's resulting from incomplete or partial cleavages. At present, this is achieved by computing all nearest-neighbour pairs for each enzyme or reagent detailed in table 1.

### Tolerance

The supplied number specifies the error allowed for mass accuracy of experimental mass determination. If no figure is specified, a default tolerance of 2 Daltons will be assumed. If you wish to specify a different tolerance then follow the qualifier '-tolerance' with the required number of Daltons. eg: '-tolerance 1'. In this case, supplied peptide masses will be matched to +/- 1 Daltons. Values of 2-4 are suggested for data obtained by laser- desorption TOF instruments. Accuracies of +/- 2 Daltons or better are generally only possible using an appropriate internal standard (e.g. oxidised insulin B chain) with TOF instruments. For electrospray or FAB data, a value of 1 can be selected in most cases. If you have real confidence in mass determination, specify '0' (zero) to limit matches to the nearest integer value (effectively +/- 0.5 Daltons). Discrimination is significantly improved by the selection of a small error tolerance.

### Whole sequence molecular weight

This option allows you to give the molwt of the whole protein (if known). This allows you to limit the search to proteins of this molwt plus/minus a 'limit' (see below). If unspecified, a whole protein molwt of 0 is assumed which emowse interprets as "search the whole database". This will include all proteins up to the maximum size of just under 700,000 Daltons. You can specify any molwt in Daltons with this command e.g. '-weight 90000'.

### Allowed whole sequence weight variability

This option is used in conjunction with the '-weight' option and is meaningless without it. It specifies a percentage. Only proteins of the given Sequence molecular weight +/- this percentage will be searched. If a Sequence molecular weight is specified but '-pcrange' is unspecified then '-pcrange ' will default to 25%. To specify a percentage of 30% use: '-pcrange 30'. In this case, a molecular weight of 90,000 Daltons was specified and the selection of 30 for the filter restricts the search to those proteins with masses from 63,000 to 117,000 Daltons. A value of 25 is suggested for initial searches, which can be progressively widened for subsequent search attempts if no matches are found. Discrimination is best when the filter percentage is narrow, but some Mw estimates (particularly from SDS gels) should be given considerable allowance for error.

### Partials factor

This specifies the weighting given to partially-cleaved peptide fragments, with a range from 0.1 to 1.0. If not specified, the default value is 0.4. The factor effectively down-weights the score awarded to a partial fragment by the specified amount. For example, a '-partials' of 0.25 will reduce the score of partial fragments to 25% (one quarter) of the score of a complete ('perfect') peptide cleavage fragment of equal mass.

Computing all possible nearest-neighbour partial fragments adds significantly to the number of peptides entered in the database (by a factor of two). The major effect of this is to increase the background score by increasing the number of random Mw matches, which can significantly reduce discrimination. The use of a low '-partials' factor (eg 0.1 - 0.3) is a useful way of limiting this effect - partial peptide matches will add a little to the cumulative frequency score, but without compromising discrimination.

More experienced users can utilise the '-partials' factor to optimize searches where the peptide Mw data contain a significant proportion of partial cleavage fragments (eg > 30%). In such cases, setting the '-partials' factor within the range 0.4 - 0.6 can help to improve discrimination. Conversely, if the digestion is perfect, with no partial fragments present, the lowest '-partials' factor of 0.1 will give maximum discrimination.

### Program requirements

The emowse search program accepts a single text file containing a list of experimentally-determined masses, generally selected from the range 700-4,000 Daltons to reduce the influence of partial cleavage products. The program outputs a ranked hit list comprising the top 30 scores, with information including the protein entry name, text identifiers, final accumulated scores, matching peptide sequences and hit versus miss tallies. User-selectable search parameters include an error tolerance (default +/- 2 Daltons), selection of the enzyme or reagent used and an intact protein Mw (optional, if known).

For each peptide Mw entry in the data file, emowse matches individual fragment molecular weights (FMWs) with database entry molecular weights (DBMWs). A 'hit' is scored when the following criterion is met:

            DBMW-tolerance-1 < FMW < DBMW+tolerance+1

If an intact protein Mw is specified (SMW) then the program prompts for a molecular weight filter percentage (MWFP). emowse then restricts the search to those entries which match the following criteria:

            R = SMW x MWFP / 100
            0 < SMW-R < emowse entry Mol.wt. < SMW+R

Default search parameters are a tolerance of +/- 2 Daltons, intact Mw specified and the MWFP set to 25.

### emowse Scoring scheme

The final scoring scheme is based on the frequency of a fragment molecular weight being found in a protein of a given range of molecular weight. OWL database sequence entries were initially grouped into 10 kDalton intact molecular weight intervals. For each 10 kDalton protein interval, peptide fragment molecular weights were assigned to cells of 100 Dalton intervals. The cells therefore contained the number of times a particular fragment molecular weight occurred in a protein of any given size. This operation was performed for each enzyme. Cell frequency values were calculated by dividing each cell value by the total number of peptides in each 10 kD protein interval. Cell frequency values for each 10 kDalton interval were then normalised to the largest cell value (Fmax), with all the cell values recalculated as:

            Cell value = Old value / Fmax

to yield floating point numbers between 0 and 1. These distribution frequency values, calculated for each cleavage reagent, were then built into the emowse search program. For every database entry scanned, all matching fragments contribute to the final score. In the current implementation, non-matching fragments are ignored (neutral). For each matching peptide Mw a score is assigned by looking up the appropriate normalised distribution frequency value. In the case of multiple 'hits' in any one target protein (i.e. more than one matching peptide Mw), the distribution frequency scores are multiplied. The final product score is inverted and then normalised to an 'average' protein Mw of 50 kDaltons to reduce the influence of random score accumulation in large proteins (>200 kDaltons). The final score is thus calculated as:

    Score = 50/(Pn x H)

Where Pn is the product of n distribution scores and H the 'hit' protein molecular weight in kD.

Important consequences of this type of scoring scheme are that matches with peptides of higher Mw carry more scoring weight, and that the non-random distribution of fragment molecular weights in proteins of different sizes is compensated for.

### Simulation studies

In a simulation of scoring properties, 100 test proteins with masses between 10 kD and 100 kD were randomly selected from the OWL sequence database. The sets of all possible tryptic peptide masses for each protein were randomized and database searches performed with increasing numbers of fragments (default search parameters) until the test protein reached the top of the ranked scoring list. 99% of the test proteins were correctly identified using only five peptides or less (mean=3.6 peptides), with one example requiring six. These figures were surprisingly small considering that some of the proteins in the test sample generated more than 100 possible tryptic fragments. All 100 test examples were identified using 30% or less of the maximum number of available peptides.

This distribution was somewhat dependent on protein size, as smaller proteins generally yield fewer peptide fragments. Thus, all proteins of 30 kD and over were identified using 13% or less of possible fragments (1 in 8), with all proteins of 40 kD and above requiring less than 10% (1 in 10). In this latter group, therefore, more than 90% of the potential information (all possible peptides) was redundant. For the simulation a 'unique' identification required matching not only of protein type (e.g. globin) but correct discrimination of type, species, and isoform or isozyme. Discrimination could be further improved by reducing the error tolerance to only +/- 1 Dalton (mean=2.7 peptides). Such accuracies are easily bettered using more sophisticated ESI/quadrupole or high-field FAB spectrometers, but the default search value (+/- 2 Daltons) compensates for the reduced accuracy obtainable from the smaller time-of-flight (TOF) instruments. Mass accuracies better than +/- 1 Dalton were not essential, and in fact the error tolerance could be relaxed to +/- 5 Daltons in many cases with little degradation in performance. The simulation thus clearly demonstrated the high degree of discrimination afforded by relatively few peptide masses, even with generous allowance for error.

## Usage

Here is a sample session with emowse:

    % emowse
    Protein identification by mass spectrometry
    Input sequence(s): sw:*
    Input file: test.mowse
    Whole sequence molwt [0]:
    Output file [100k_rat.emowse]:

## Command line arguments

       Mandatory qualifiers:
      [-sequences]         seqall     Sequence database USA
      [-infile]            infile     Name of molecular weight data file
       -weight             integer    Whole sequence molwt
       -outfile            outfile    Output file name

       Optional qualifiers: (none)
       Advanced qualifiers:
       -enzyme             menu       Enzyme or reagent
       -aadata             string     Molecular weight data for amino acids
       -pcrange            integer    Allowed whole sequence weight variability
       -frequencies        string     Frequencies file
       -tolerance          float      (no help text) float value
       -partials           float      Partials factor

       General qualifiers:
      -help                bool       report command line options. More
                                      information on associated and general
                                      qualifiers can be found with -help -verbose

Mandatory qualifiers | Allowed values | Default
--- | --- | ---
[-sequences] (Parameter 1) | Sequence database USA | Readable sequence(s) | Required
[-infile] (Parameter 2) | Name of molecular weight data file | Input file | Required
-weight | Whole sequence molwt | Any integer value | 0
-outfile | Output file name | Output file | <sequence>.emowse
Optional qualifiers | Allowed values | Default
(none)
Advanced qualifiers | Allowed values | Default
-enzyme | Enzyme or reagent |
1 | (Trypsin)
2 | (Lys-C)
3 | (Arg-C)
4 | (Asp-N)
5 | (V8-bicarb)
6 | (V8-phosph)
7 | (Chymotrypsin)
8 | (CNBr)
| 1
-aadata | Molecular weight data for amino acids | Any string is accepted | Eamino.dat
-pcrange | Allowed whole sequence weight variability | Integer from 0 to 75 | 25
-frequencies | Frequencies file | Any string is accepted | Efreqs.dat
-tolerance | (no help text) float value | Number from 0.100 to 1.000 | 0.1
-partials | Partials factor | Number from 0.100 to 1.000 | 0.4

## Input file format

The input file is a list of molecular weights of the peptide fragments. One weight is allowed per line. For example, some weights taken from a Trypsin digest of the protein sw:100K_rat (produced by using the program digest are):

    6082.8
    5423.0
    3086.3
    2930.3
    2424.7
    2030.2
    1399.6
    1086.2

Each molecular weight must be on a line of its own. Masses (M not M[H+]) are accepted in any order (ascending,descending or mixed). Peptide masses can be entered as integers or floating-point values, the latter being rounded to the nearest integer value for the search.

It is suggested that peptide masses should be selected from the range 700-4000 Daltons. This range balances the fact that very small peptides give little discrimination and minimizes the frequency of partially-cleaved peptides.

As a general rule, users are advised to identify and remove peptide masses resulting from autodigestion of the cleavage enzyme (e.g tryptic fragments of trypsin), best obtained by MS analysis of control digests containing only the enzyme.

Further information on the partial sequence and/or composition of the peptides can be given after the weight with a 'seq()' or 'comp()' specification. This should be formatted like:

    mw seq(...) comp(...)

where mw is the molecular mass of the fragment, `seq(...)` is sequence information and `comp(...)` is composition information. A line may contain more than one sequence information qualifiers. For example:

###

###

##

###

###

###

##

##

##

###

##

##

##

##

##

##

##

##

##

    7176 seq(b-t[pqt]ln)
    1744
    1490
    1433   comp(3[ed]1[p]) seq(gmde)

    Sequence information
    The sequence information should be given in standard
    One-character code. It should be preceded by a prefix
    as outlined in the table below, to indicate what type of sequence
    it is.

    Prefixes to use with sequence information for
    emowse
    PrefixMeaningExample
    b-N->C sequence
    seq(b-DEFG)
    y-C->N sequence
    seq(y-GFED)
    *-
    Orientation unknown
    seq(*-DEFG)
    seq(*-GFED)
    n-N terminal sequence
    seq(n-ACDE)
    c-C terminal sequence
    seq(c-FGHI)
    The examples are all correct data for a
    peptide with a sequence ACDEFGHI.
     Note that *-DEFG
    will search for both DEFG and GFED

    Both lower and upper case characters may be used for amino-acids.
    An unknown amino acid may be indicated by an 'X'.
    More than one amino acid may be specified for a position by
    putting them between square brackets.
    A line may contain several sequence information
    qualifiers. An example for a peptide with the actual
    sequence ACDEFGHI might look like:

    12345 seq(n-AC[DE]) seq(c-HI)

    Composition Information
    Composition should consist of a number, followed by the
    corresponding amino acid between square brackets.
    For example
    comp(2[H]0[M]3[DE]*[K]) indicates
    a peptide which contains 2 histidines, no methionines,
    3 acidic residues (glutamic or aspartic acid) and
    at least 1 lysine.

        Output file format

    The emowse search program outputs a listing file  containing the following information.

    Specified search parameters

            Includes all specified parameters such as digest reagent,
      specified error tolerance, specified intact protein Mw and Mw filter
      percentage. All supplied peptide Mws are listed in descending order,
      followed by the total number of entries scanned during the search.

    Short 'hit' listing

            The top 50 scoring proteins are then listed in descending
      order, details include the sequence ID name and brief text
     identifiers. Details are limited to the top 50 scores as a deliberate
      compromise to keep the result listings as short as possible.

    Detailed 'hit' listing

            The top 50 entries are then listed in more detail.The first
      line includes the sequence ID name, the emowse search score
      (typically a few powers of 10), the 'hit' protein Mw and finally
      an 'accuracy' ratio calculated by dividing 'hits' by the total
      number of peptides used for the search. This cannot be used to
      ascribe significance, but experience has shown that anything below
      0.3 is generally not worth pursuing. Line 2 is the protein
      text identifier. Subsequent lines list 'hit' and 'miss' peptides,
      with the appropriate start, end and corresponding sequences of correct
      peptide matches.  'miss' peptides are indicated by 'No match' at the
    start of the last line for that protein.

            Matching peptides marked with a '*' denote partially-cleaved
      fragments.

    This is the output from search all of the SwissProt database with the
    input file above:

    Using data fragments of:
              1086.2
              1399.6
              2030.2
              2424.7
              2930.3
              3086.3
              5423.0
              6082.8

    1   100K_RAT     100 KDA PROTEIN (EC 6.3.2.-).
    2   POLG_MCFA    GENOME POLYPROTEIN [CONTAINS: CAPSID PROTEIN C (CORE PROTEIN);
    3   PGCV_HUMAN   VERSICAN CORE PROTEIN PRECURSOR (LARGE FIBROBLAST PROTEOGLYCAN
    4   POL1_BAYMJ   GENOME POLYPROTEIN 1 [CONTAINS: CYTOPLASMIC INCLUSION PROTEIN
    5   RRPB_CVMJH   RNA-DIRECTED RNA POLYMERASE (EC 2.7.7.48) (ORF1B).
    6   DMD_HUMAN    DYSTROPHIN.
    7   STRH_STRPN   BETA-N-ACETYLHEXOSAMINIDASE PRECURSOR (EC 3.2.1.52).
    8   NGCA_CHICK   NEURONAL-GLIAL CELL ADHESION MOLECULE PRECURSOR (NG-CAM).
    9   RIR1_ASFB7   RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE LARGE CHAIN (EC 1.17.4.1)
    10  YMW6_YEAST   HYPOTHETICAL 147.0 KDA PROTEIN IN ABF2-CHL12 INTERGENIC REGION
    11  UBR1_YEAST   N-END-RECOGNIZING PROTEIN (UBIQUITIN-PROTEIN LIGASE E3 COMPONE
    12  MCR_RAT      MINERALOCORTICOID RECEPTOR (MR).
    13  CD8A_FELCA   T-CELL SURFACE GLYCOPROTEIN CD8 ALPHA CHAIN PRECURSOR.
    14  YM27_MYCTU   HYPOTHETICAL 26.6 KDA PROTEIN RV2227.
    15  CD52_MACFA   CAMPATH-1 ANTIGEN PRECURSOR (CD52 ANTIGEN) (CDW52) (CAMBRIDGE
    16  POL1_BAYMG   GENOME POLYPROTEIN 1 [CONTAINS: CYTOPLASMIC INCLUSION PROTEIN
    17  CP7B_RAT     CYTOCHROME P450 7B1 (OXYSTEROL 7-ALPHA-HYDROXYLASE) (EC 1.14.1
    18  CCAE_RAT     VOLTAGE-DEPENDENT R-TYPE CALCIUM CHANNEL ALPHA-1E SUBUNIT (CAL
    19  CCAE_MOUSE   VOLTAGE-DEPENDENT R-TYPE CALCIUM CHANNEL ALPHA-1E SUBUNIT (CAL
    20  GCST_MYCTU   PROBABLE AMINOMETHYLTRANSFERASE (EC 2.1.2.10) (GLYCINE CLEAVAG
    21  LYST_HUMAN   LYSOSOMAL TRAFFICKING REGULATOR (BEIGE HOMOLOG).
    22  FIXI_BRAJA   NITROGEN FIXATION PROTEIN FIXI (E1-E2 TYPE CATION ATPASE FIXI)
    23  MAP4_MOUSE   MICROTUBULE-ASSOCIATED PROTEIN 4.
    24  RAD3_SCHPO   DNA REPAIR PROTEIN RAD3.
    25  MTHR_SCHPO   PROBABLE METHYLENETETRAHYDROFOLATE REDUCTASE 1 (EC 1.5.1.20).
    26  BCA1_RAT     CRK-ASSOCIATED SUBSTRATE (P130CAS) (BREAST CANCER ANTI-ESTROGE
    27  G6PE_RABIT   GDH/6PGL ENDOPLASMIC BIFUNCTIONAL PROTEIN [INCLUDES: GLUCOSE 1
    28  MRP3_RAT     CANALICULAR MULTISPECIFIC ORGANIC ANION TRANSPORTER 2 (MULTIDR
    29  PTVB_ECOLI   PTS SYSTEM, FRUCTOSE-LIKE-1 IIBC COMPONENT (PHOSPHOTRANSFERASE
    30  YMHA_CAEEL   HYPOTHETICAL 83.2 KDA PROTEIN F58A4.11 IN CHROMOSOME III.
    31  DAB_DROME    DISABLED PROTEIN.
    32  EGLN_HUMAN   ENDOGLIN PRECURSOR (CD105 ANTIGEN).
    33  DPOZ_YEAST   DNA POLYMERASE ZETA CATALYTIC SUBUNIT (EC 2.7.7.7).
    34  C166_BRARE   CD166 ANTIGEN HOMOLOG PRECURSOR (NEUROLIN) (DM-GRASP HOMOLOG).
    35  YAHB_ECOLI   HYPOTHETICAL TRANSCRIPTIONAL REGULATOR IN BETT-PRPR INTERGENIC
    36  ACSB_ACEXY   CELLULOSE SYNTHASE 93 KDA SUBUNIT PRECURSOR (CELLULOSE SYNTHAS
    37  CIN5_RAT     SODIUM CHANNEL PROTEIN, CARDIAC MUSCLE ALPHA-SUBUNIT.
    38  SUIS_SUNMU   SUCRASE-ISOMALTASE, INTESTINAL [CONTAINS: SUCRASE (EC 3.2.1.48
    39  TEGP_HSVEA   PROBABLE TEGUMENT PHOSPHOPROTEIN (ORF5) (FRAGMENT).
    40  YDT2_SCHPO   HYPOTHETICAL 217.4 KDA PROTEIN C6B12.02C IN CHROMOSOME I.
    41  YHFC_ECOLI   HYPOTHETICAL 43.2 KDA PROTEIN IN PPIA-NIRB INTERGENIC REGION (
    42  TBX5_HUMAN   TBX5 PROTEIN (T-BOX PROTEIN 5).
    43  YEX0_YEAST   HYPOTHETICAL 64.8 KDA PROTEIN IN GDI1-COX15 INTERGENIC REGION.
    44  Y323_MYCPN   HYPOTHETICAL PROTEIN MG323 HOMOLOG.
    45  VP42_ROTS1   OUTER CAPSID PROTEIN VP4 (HEMAGGLUTININ) (OUTER LAYER PROTEIN
    46  NOEC_AZOCA   NODULATION PROTEIN NOEC.
    47  BIB_DROME    NEUROGENIC PROTEIN BIG BRAIN.
    48  NB35_YEAST   NBP35 PROTEIN.
    49  HSCA_RICPR   CHAPERONE PROTEIN HSCA HOMOLOG.
    50  SYL_AERPE    LEUCYL-TRNA SYNTHETASE (EC 6.1.1.4) (LEUCINE--TRNA LIGASE) (LE

        1  : 100K_RAT       1.277e+06 100368.6   0.750
             100 KDA PROTEIN (EC 6.3.2.-).
             Mw     Start  End    Seq
             1086.3 358    367    CATTPMAVHR
             1399.6 6      17     GDFLNYALSLMR
             2424.7 290    312    VFMEDVGAEPGSILTELGGFEVK
             2930.3 671    698    QLILASQSSDADAVFSAMDLAFAVDLCK
             3086.3 458    485    QLSIDTRPFRPASEGNPSDDPDPLPAHR
            *6082.8 817    870    QDLVYFWTSSPSLPASEEGFQPMPSITIRPPDDQHLPTANTCISR...
             No Match      2030.2 5423.0

        2  : POLG_MCFA      2.612e+05 373265.6   0.500
             GENOME POLYPROTEIN [CONTAINS: CAPSID PROTEIN C (CORE PROTEIN); MATRIX PROTEIN (ENVELOPE PROTEIN M); MAJOR ENVELOPE PROTEIN E; NONSTRUCTURAL PROTEINS NS1, NS2A, NS2B, NS4A AND NS4B; HELICASE (NS3); RNA-DIRECTED RNA POLYMERASE (EC 2.7.7.48) (NS5)].
             Mw     Start  End    Seq
             2423.7 3233   3251   TSWSVHQYHEWMTTDDMLR
             2931.2 951    977    EYTPDTLSDPSDQALFIPPAWGGPISR
            *3088.7 2174   2200   SYMDSDLVKWVILGSCLICGVLAWEMR
             6084.9 1327   1382   AHQPTVAAVLAFTMVVLFLYMEQTNVSMELEFISAGETPEGVSTE...
             No Match      1086.2 1399.6 2030.2 5423.0

        3  : PGCV_HUMAN     2.202e+05 372819.0   0.625
             VERSICAN CORE PROTEIN PRECURSOR (LARGE FIBROBLAST PROTEOGLYCAN) (CHONDROITIN SULFATE PROTEOGLYCAN CORE PROTEIN 2) (GLIAL HYALURONATE- BINDING PROTEIN) (GHAP).
             Mw     Start  End    Seq
             1398.5 651    662    TEIELFPYSGDK
            *2029.2 1334   1352   TGRMSDLSVIGHPIDSESK
             2426.6 842    863    DIPSFTEDGADEFTLIPDSTQK
            *2928.3 1190   1216   ATELIEFSTIKVTVPSDITTAFSSVDR
             6081.6 3037   3092   ILDSNDQATVNPVEFNTEVATPPFSLLETSNETDFLIGINEESVE...
             No Match      1086.2 3086.3 5423.0

        4  : POL1_BAYMJ     5.410e+04 270769.3   0.500
             GENOME POLYPROTEIN 1 [CONTAINS: CYTOPLASMIC INCLUSION PROTEIN (CI); RNA-DIRECTED RNA POLYMERASE (EC 2.7.7.48); COAT PROTEIN (CP)].
             Mw     Start  End    Seq
            *2031.3 368    385    ISRLSSYLLDDHQGIASR
            *2423.7 1531   1551   RNEFQPFTQEVVDFINGPGTK
             5422.0 1970   2016   FAISPQFDEEFGHDFSPELVELGLTYEFDDITSDICENPYMSLTM...
             6077.8 1552   1606   IPYCPWVFDRPACGYASHTALFEKPTTLTDIIHMQASDGLHNINN...
             No Match      1086.2 1399.6 2930.3 3086.3

        5  : RRPB_CVMJH     4.449e+04 308836.3   0.625
             RNA-DIRECTED RNA POLYMERASE (EC 2.7.7.48) (ORF1B).
             Mw     Start  End    Seq
            *1085.4 639    648    IVSSLVLARK
             2030.2 172    187    DWYDFVENPDIINVYK
             2422.7 414    433    FQTVKPGNFNQDFYEFILSK
            *2932.2 2162   2187   YTDLQCIESLNVLFDGRDNGALEAFK
             6077.9 662    721    LANECAQVLGEIVMCGGCYYVKPGGTSSGDATTAFANSVFNICQA...
             No Match      1399.6 3086.3 5423.0

        6  : DMD_HUMAN      3.824e+04 426675.4   0.625
             DYSTROPHIN.
             Mw     Start  End    Seq
            *1399.6 436    447    VASMEKQSNLHR
             2031.3 2478   2494   AWTELTDWLSLLDQVIK
             2426.6 1165   1183   DLSEMHEWMTQAEEEYLER
            *3083.4 1159   1183   TVSLQKDLSEMHEWMTQAEEEYLER
             5428.2 1979   2026   EETMMVMTEDMPLEISYVPSTYLTEITHVSQALLEVEQLLNAPDL...
             No Match      1086.2 2930.3 6082.8

        7  : STRH_STRPN     2.144e+04 144521.5   0.625
             BETA-N-ACETYLHEXOSAMINIDASE PRECURSOR (EC 3.2.1.52).
             Mw     Start  End    Seq
             1400.6 827    839    FAEYANTLAAMAK
             2029.2 655    673    ASELGYSDVHLLLGNDGLR
             2423.9 729    751    DIGLIPAINSPGHMDAMLVAMEK
            *2930.4 1280   1308   LPETGTHDSAGLVVAGLMSTLAAYGLTKR
             3089.2 255    281    GTNDYYNDPNGNHLTESQMTDLINYAK
             No Match      1086.2 5423.0 6082.8

        8  : NGCA_CHICK     1.849e+04 136570.2   0.375
             NEURONAL-GLIAL CELL ADHESION MOLECULE PRECURSOR (NG-CAM).
             Mw     Start  End    Seq
             2930.1 1036   1062   GGFHGAAVEFGAAQEDDVEFEVQFMNK
            *3087.4 110    138    CFATNALGTAVSPEANVIAENTPQWPKEK
             6077.2 1      57     MALPMVGLLLLLLLGGPGAAITIPPEYGAHDFLQPPELTEEPPEQ...
             No Match      1086.2 1399.6 2030.2 2424.7 5423.0

        9  : RIR1_ASFB7     1.768e+04 87491.8    0.375
             RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE LARGE CHAIN (EC 1.17.4.1) (RIBONUCLEOTIDE REDUCTASE).
             Mw     Start  End    Seq
            *2423.6 568    589    CGDLSSSWEERVAQTTQGVLTR
             2931.3 407    433    SNLSHVGTITNSNLCIEVTIPCWEGDK
             5422.1 243    289    SNGIQNYIMLQNASQCYANQGGLRPGAYAVYLELWHQDIFTFLQM...
             No Match      1086.2 1399.6 2030.2 3086.3 6082.8

        10 : YMW6_YEAST     1.760e+04 147040.9   0.375
             HYPOTHETICAL 147.0 KDA PROTEIN IN ABF2-CHL12 INTERGENIC REGION.
             Mw     Start  End    Seq
             2028.4 977    993    FLPLVFFTAYEPDVELK
             3086.6 135    161    SIVLLADLPSSNNLLIELFHIFYDPNK
             5423.0 441    485    EIWEIIDTIPSTLYNLYYINDLNINEQVDSVIFEYLLPFEPDNDK
             No Match      1086.2 1399.6 2424.7 2930.3 6082.8

        11 : UBR1_YEAST     1.661e+04 224837.6   0.375
             N-END-RECOGNIZING PROTEIN (UBIQUITIN-PROTEIN LIGASE E3 COMPONENT) (N- RECOGNIN).
             Mw     Start  End    Seq
            *1400.6 258    268    EMTQQGKMYER
             3089.3 939    965    SVPDYLTEDTTEFDEALEEVSVFVEPK
             5421.5 1830   1881   IPPTDEDDEDMEEGEDGFFTEGNDEMDVDDETGQAANLFGVGAEG...
             No Match      1086.2 2030.2 2424.7 2930.3 6082.8

        12 : MCR_RAT        1.463e+04 106736.9   0.375
             MINERALOCORTICOID RECEPTOR (MR).
             Mw     Start  End    Seq
            *2031.2 19     36     WSQVSQTLERSSLGPAER
             3088.4 466    495    DYYSLSGILGPPVPGFDGSCEDSAFPVGIK
             5423.0 191    244    SSSVSSPLNMASSVCSPVGINSMSSSTTSFGSFPVHSPITQGTSL...
             No Match      1086.2 1399.6 2424.7 2930.3 6082.8

        13 : CD8A_FELCA     1.074e+04 26120.3    0.250
             T-CELL SURFACE GLYCOPROTEIN CD8 ALPHA CHAIN PRECURSOR.
             Mw     Start  End    Seq
             2422.8 42     63     VELQCEVLLSSAAPGCTWLFQK
             5421.2 112    160    EEEGYYFCSVVSNSVLYFSAFVPVFLPVKPTTTPAPRPPTQAPIT...
             No Match      1086.2 1399.6 2030.2 2930.3 3086.3 6082.8

        14 : YM27_MYCTU     1.054e+04 26614.4    0.250
             HYPOTHETICAL 26.6 KDA PROTEIN RV2227.
             Mw     Start  End    Seq
             2426.6 99     120    EAPWPDSLDDWLASCHAAGQTR
             5424.0 128    174    YGTNDWNALHQDLYGELVFPLQVVINLSDPETDYTGGEFLLVEQR...
             No Match      1086.2 1399.6 2030.2 2930.3 3086.3 6082.8

        15 : CD52_MACFA     1.038e+04 6502.6     0.125
             CAMPATH-1 ANTIGEN PRECURSOR (CD52 ANTIGEN) (CDW52) (CAMBRIDGE PATHOLOGY 1 ANTIGEN).
             Mw     Start  End    Seq
             6087.0 4      60     FLFLLLTISLLVMVQIQTGVTSQNATSQSSPSASSNLSGGGFLFF...
             No Match      1086.2 1399.6 2030.2 2424.7 2930.3 3086.3 5423.0

        16 : POL1_BAYMG     9.354e+03 270875.5   0.625
             GENOME POLYPROTEIN 1 [CONTAINS: CYTOPLASMIC INCLUSION PROTEIN (CI); RNA-DIRECTED RNA POLYMERASE (EC 2.7.7.48); COAT PROTEIN (CP)].
             Mw     Start  End    Seq
            *1398.5 899    909    DEIPHELRYAR
            *2031.2 1308   1325   MEISQHDPDFLKQNGSGK
            *2423.8 910    931    VPFSVTTLSKFDWPALALACEK
             5422.0 1972   2018   FAISPQFDEEFGHDFSPELVELGLTYEFDDITSDICENPYMSLTM...
            *6082.9 550    603    MGDHCIQVMTYGSALQCHAMDPSFISTFDAIFLDEAHDVKEHSLV...
             No Match      1086.2 2930.3 3086.3

        17 : CP7B_RAT       9.319e+03 48226.8    0.375
             CYTOCHROME P450 7B1 (OXYSTEROL 7-ALPHA-HYDROXYLASE) (EC 1.14.13.-) (HCT-1) (FRAGMENT).
             Mw     Start  End    Seq
             2030.4 249    266    EQLDSLVCLESAILEVLR
            *2928.4 85     110    VFDFCSSLVFEITFTTIYGKILAANK
             5421.2 179    224    YYGHEEFEIGAHHLGLLWASLANTIPAMFWAMYYLLQHPEAMEVL...
             No Match      1086.2 1399.6 2424.7 3086.3 6082.8

        18 : CCAE_RAT       9.273e+03 252115.4   0.375
             VOLTAGE-DEPENDENT R-TYPE CALCIUM CHANNEL ALPHA-1E SUBUNIT (CALCIUM CHANNEL, L TYPE, ALPHA-1 POLYPEPTIDE, ISOFORM 6) (RBE-II) (RBE2) (BRAIN CALCIUM CHANNEL II) (BII).
             Mw     Start  End    Seq
             2424.9 1711   1731   IHYTEMYEMLTLMSPPLGLGK
            *5424.5 1349   1393   MEMSIFYVVYFVVFPFFFVNIFVALIIITFQEQGDKMMEECSLEK
             6081.2 426    477    SQVFYWIVLSVVALNTACVAIVHHNQPQWLTHLLYYAEFLFLGLF...
             No Match      1086.2 1399.6 2030.2 2930.3 3086.3

        19 : CCAE_MOUSE     9.088e+03 257235.0   0.375
             VOLTAGE-DEPENDENT R-TYPE CALCIUM CHANNEL ALPHA-1E SUBUNIT (CALCIUM CHANNEL, L TYPE, ALPHA-1 POLYPEPTIDE, ISOFORM 6) (BRAIN CALCIUM CHANNEL II) (BII).
             Mw     Start  End    Seq
             2424.9 1762   1782   IHYTEMYEMLTLMSPPLGLGK
            *5424.5 1400   1444   MEMSIFYVVYFVVFPFFFVNIFVALIIITFQEQGDKMMEECSLEK
             6081.2 476    527    SQVFYWIVLSVVALNTACVAIVHHNQPQWLTHLLYYAEFLFLGLF...
             No Match      1086.2 1399.6 2030.2 2930.3 3086.3

        20 : GCST_MYCTU     8.954e+03 39628.9    0.250
             PROBABLE AMINOMETHYLTRANSFERASE (EC 2.1.2.10) (GLYCINE CLEAVAGE SYSTEM T PROTEIN).
             Mw     Start  End    Seq
             3085.4 30     58     ELGASFAEFGGWLMPVSYAGTVSEHNATR
             5422.1 307    360    GVLRPGLAVLVGDETVGVTTSGTFSPTLQVGIGLALIDSDAGIED...
             No Match      1086.2 1399.6 2030.2 2424.7 2930.3 6082.8

        21 : LYST_HUMAN     8.339e+03 429123.8   0.625
             LYSOSOMAL TRAFFICKING REGULATOR (BEIGE HOMOLOG).
             Mw     Start  End    Seq
             1400.6 3733   3743   LWSTWDLKPVR
            *2031.2 690    705    WDALKAYQNFVFEEDR
            *2928.2 2981   3006   SEDVVKPPLSYLFEDKTHSSFSSTVK
             3086.5 3703   3732   EIICSVAFSNQPEGVSINVIAGGLENGIVR
            *5424.1 3106   3151   VRDDVYHNILTNNLPNLLEYGNITALTNLWYTGQITNFEYLTHLN...
             No Match      1086.2 2424.7 6082.8

        22 : FIXI_BRAJA     7.585e+03 77338.3    0.250
             NITROGEN FIXATION PROTEIN FIXI (E1-E2 TYPE CATION ATPASE FIXI) (EC 3.6.1.-).
             Mw     Start  End    Seq
             2932.4 244    271    FVGPDEISQVPVAAISPGDIVLLRPGER
             6087.3 356    415    LYAPVVHATALITILGWVIAGASWHDAIVTGVAVLIITCPCALGL...
             No Match      1086.2 1399.6 2030.2 2424.7 3086.3 5423.0

        23 : MAP4_MOUSE     7.184e+03 117675.3   0.250
             MICROTUBULE-ASSOCIATED PROTEIN 4.
             Mw     Start  End    Seq
             3087.5 431    458    DVTLPLEAERPLVTDMTPSLETEMTLGK
             6085.7 272    327    DIEEITKPDVILANVTQPSTESDMFLAQDMELLTGTEAAHANNII...
             No Match      1086.2 1399.6 2030.2 2424.7 2930.3 5423.0

        24 : RAD3_SCHPO     6.503e+03 121973.3   0.250
             DNA REPAIR PROTEIN RAD3.
             Mw     Start  End    Seq
             3085.4 860    888    LQPLYVDAATAIANTGAHSAYDCYDILSK
             6087.7 713    765    VLQEIYAGIDDPDEIEAVSLNFHDYSFDQQLLLHENSGTWDSALS...
             No Match      1086.2 1399.6 2030.2 2424.7 2930.3 5423.0

        25 : MTHR_SCHPO     6.242e+03 69012.0    0.375
             PROBABLE METHYLENETETRAHYDROFOLATE REDUCTASE 1 (EC 1.5.1.20).
             Mw     Start  End    Seq
             1399.4 118    129    DTDWTEGESGFR
            *3085.5 400    426    ISSLPWSDLPISDEADLIRDQLLSMNR
             6079.9 43     98     TWGRPMFVDVTWGAGGTSSELTPGIVNVIQTDFEVDTCMHLTCTN...
             No Match      1086.2 2030.2 2424.7 2930.3 5423.0

        26 : BCA1_RAT       5.803e+03 104261.8   0.375
             CRK-ASSOCIATED SUBSTRATE (P130CAS) (BREAST CANCER ANTI-ESTROGEN RESISTANCE 1 PROTEIN).
             Mw     Start  End    Seq
            *1399.5 14     26     RAGGLEDVSWGPR
             5422.9 249    299    QTPHHSFPSPATDLYQVPPGPGSPAQDIYQVPPSAGTGHDIYQVP...
            *6086.8 422    477    EETYDVPPAFAKPKPFDPTRHPLILAAPPPDSPPAEDVYDVPPPA...
             No Match      1086.2 2030.2 2424.7 2930.3 3086.3

        27 : G6PE_RABIT     5.630e+03 85285.1    0.250
             GDH/6PGL ENDOPLASMIC BIFUNCTIONAL PROTEIN [INCLUDES: GLUCOSE 1- DEHYDROGENASE (EC 1.1.1.47) (HEXOSE-6-PHOSPHATE DEHYDROGENASE); 6- PHOSPHOGLUCONOLACTONASE (EC 3.1.1.31) (6PGL)].
             Mw     Start  End    Seq
             2929.4 453    477    ESFVPTEHLLASWVFWTPLLESLAR
             5428.1 564    614    VGTFHLALSGGSSPIALFQQLASGHYGFPVPLSDPESNFQGLQAH...
             No Match      1086.2 1399.6 2030.2 2424.7 3086.3 6082.8

        28 : MRP3_RAT       5.465e+03 168977.6   0.625
             CANALICULAR MULTISPECIFIC ORGANIC ANION TRANSPORTER 2 (MULTIDRUG RESISTANCE-ASSOCIATED PROTEIN 3) (MRP-LIKE PROTEIN-2) (MLP-2).
             Mw     Start  End    Seq
             1086.2 279    288    IAGEDEVLLK
             2426.8 1494   1517   GVVAEFDSPVNLIAAGGIFYGMAK
            *2930.4 1359   1384   SQLTIIPQDPILFSGTLRMNLDPFGR
            *3087.5 757    785    VSLARAVYSDANIFLLDDPLSAVDSHVAK
            *6086.0 165    217    ILDPFRFTTFYIYFALVLCAFILSCFQEKPPLFSPENLDTNPCPE...
             No Match      1399.6 2030.2 5423.0

        29 : PTVB_ECOLI     5.278e+03 51322.6    0.250
             PTS SYSTEM, FRUCTOSE-LIKE-1 IIBC COMPONENT (PHOSPHOTRANSFERASE ENZYME II, BC COMPONENT) (EC 2.7.1.69).
             Mw     Start  End    Seq
             3084.7 340    368    HIYDWYAIVGVVALMPPVAAGLATFIAPK
             5419.7 257    306    ALQPLLGSMLIPFVTLLVFGVLTYYVIGPVMSDLMGGLLHFLNTI...
             No Match      1086.2 1399.6 2030.2 2424.7 2930.3 6082.8

        30 : YMHA_CAEEL     5.268e+03 83221.0    0.375
             HYPOTHETICAL 83.2 KDA PROTEIN F58A4.11 IN CHROMOSOME III.
             Mw     Start  End    Seq
            *1400.6 277    288    SVFSTNLKVHLR
             2030.2 559    579    GGGNVTTPPTPNSSSFPSTPK
             5428.2 5      50     LFVFGSGADDPSHFNYYHCSDLILSSTFSSFSFLILIYLYIFIFY...
             No Match      1086.2 2424.7 2930.3 3086.3 6082.8

        31 : DAB_DROME      5.168e+03 264048.0   0.500
             DISABLED PROTEIN.
             Mw     Start  End    Seq
             2029.1 1588   1604   MNSCDEDYDYDGEFVAR
            *2423.5 2159   2179   FDDNVKVSQFDDAAFEDDFAK
            *3087.6 1018   1045   LNVPASKLSTMTLVQLTAYLSEYLSSEK
             5426.0 2305   2357   CVNDTTFILPSQSLLSAAATAQPATELESPCLLQLASPAVAGASE...
             No Match      1086.2 1399.6 2930.3 6082.8

        32 : EGLN_HUMAN     4.635e+03 70577.9    0.250
             ENDOGLIN PRECURSOR (CD105 ANTIGEN).
             Mw     Start  End    Seq
             2930.4 305    333    MLNASIVASFVELPLASIVSLHASSCGGR
             5418.3 94     143    EVLLVLSVNSSVFLHLQALGIPLHLAYNSSLVTFQEPPGVNTTEL...
             No Match      1086.2 1399.6 2030.2 2424.7 3086.3 6082.8

        33 : DPOZ_YEAST     4.530e+03 172956.7   0.375
             DNA POLYMERASE ZETA CATALYTIC SUBUNIT (EC 2.7.7.7).
             Mw     Start  End    Seq
             1398.7 1169   1180   VTQNNPKPIFLK
             2028.4 1358   1375   LFNLIGINVGNWAQEIVK
             6078.9 730    780    IQHCINEIPVMFYESEFEMFEALTDLVLLLDPDILSGFEIHNFSW...
             No Match      1086.2 2424.7 2930.3 3086.3 5423.0

        34 : C166_BRARE     4.297e+03 61273.4    0.250
             CD166 ANTIGEN HOMOLOG PRECURSOR (NEUROLIN) (DM-GRASP HOMOLOG).
             Mw     Start  End    Seq
             3085.5 306    334    CSLLDNDVMESTQIVTVSFLDASLTPTGK
             5426.4 1      52     MHSVICLFGAFIAAALFAPGSCLPTVIGLYGETIEVPCNNGNNKP...
             No Match      1086.2 1399.6 2030.2 2424.7 2930.3 6082.8

        35 : YAHB_ECOLI     4.268e+03 34865.9    0.250
             HYPOTHETICAL TRANSCRIPTIONAL REGULATOR IN BETT-PRPR INTERGENIC REGION.
             Mw     Start  End    Seq
             2029.3 1      18     MNSIFTEENLLAFTTAAR
             5424.0 121    171    QFPTCQITVTTEVYNGVWDAIINNQANIAIGAPDTLLDGGGIDYT...
             No Match      1086.2 1399.6 2424.7 2930.3 3086.3 6082.8

        36 : ACSB_ACEXY     4.019e+03 85381.9    0.500
             CELLULOSE SYNTHASE 93 KDA SUBUNIT PRECURSOR (CELLULOSE SYNTHASE PROTEIN B).
             Mw     Start  End    Seq
             1087.2 186    195    LNFSFASSSK
             2424.8 541    562    MPNLAFMASAGYPFTTYADLSR
            *2928.4 359    385    MDVAPIDVGARVAYDAPSFIPTNRPVR
             3083.5 739    764    SSPLYTVGTVPLWLEPDWYMHNHPSR
             No Match      1399.6 2030.2 5423.0 6082.8

        37 : CIN5_RAT       3.905e+03 227366.6   0.375
             SODIUM CHANNEL PROTEIN, CARDIAC MUSCLE ALPHA-SUBUNIT.
             Mw     Start  End    Seq
            *2425.7 661    682    QRALSAVSVLTSALEELEESHR
             2928.0 1096   1122   AWSQVSETTSSEAGASTSQADWQQEQK
             3084.8 251    278    LADVMVLTVFCLSVFALIGLQLFMGNLR
             No Match      1086.2 1399.6 2030.2 5423.0 6082.8

        38 : SUIS_SUNMU     3.806e+03 208173.0   0.500
             SUCRASE-ISOMALTASE, INTESTINAL [CONTAINS: SUCRASE (EC 3.2.1.48); ISOMALTASE (EC 3.2.1.10)].
             Mw     Start  End    Seq
            *2028.3 365    381    IPFDAQVTDIDYMEDKK
             2424.7 1551   1571   QDPVSWNETFASMSTDILNIR
             3086.4 1226   1250   QLYEDMVSAQIPYDVQYTDIDYMER
            *6083.9 301    354    VIGGILDFYIFLGDTPGQVVQQYQELTGRPAMPSYWSLGFQLSRW...
             No Match      1086.2 1399.6 2930.3 5423.0

        39 : TEGP_HSVEA     3.789e+03 7633.1     0.125
             PROBABLE TEGUMENT PHOSPHOPROTEIN (ORF5) (FRAGMENT).
             Mw     Start  End    Seq
             5418.5 22     76     GSGMSDQEVSEEQSAGDAWVSAAMAAAEAVAAAATSTGIDNTNDY...
             No Match      1086.2 1399.6 2030.2 2424.7 2930.3 3086.3 6082.8

        40 : YDT2_SCHPO     3.706e+03 217433.0   0.500
             HYPOTHETICAL 217.4 KDA PROTEIN C6B12.02C IN CHROMOSOME I.
             Mw     Start  End    Seq
            *1398.6 1073   1083   LQPLHSRQYTR
            *2422.9 1461   1482   SVHLNLLTAVFCNMAKLYADAK
             5421.9 1483   1530   TNGFASSQYLQSLFIHYLSSLLSSMQHSYETNGHSSDTHSLFVIN...
            *6083.6 1477   1530   LYADAKTNGFASSQYLQSLFIHYLSSLLSSMQHSYETNGHSSDTH...
             No Match      1086.2 2030.2 2930.3 3086.3

        41 : YHFC_ECOLI     3.697e+03 43166.3    0.250
             HYPOTHETICAL 43.2 KDA PROTEIN IN PPIA-NIRB INTERGENIC REGION (O393).
             Mw     Start  End    Seq
             5418.4 273    323    ILTVLAGLAAILMYVFNTGTPAHMAWSILALGFFSSAIYTTIITL...
            *6083.3 329    385    LVNFVLTCGTIGTMLTFVVTGPIVEHSGPQAALLTANGLYAVVFV...
             No Match      1086.2 1399.6 2030.2 2424.7 2930.3 3086.3

        42 : TBX5_HUMAN     3.628e+03 57438.9    0.250
             TBX5 PROTEIN (T-BOX PROTEIN 5).
             Mw     Start  End    Seq
             2028.3 1      19     MADADEALAGAHLWSLTQK
             6083.7 373    429    QACMYASSAPPSEPVPSLEDISCNTWPSMPSYSSCTVTTVQPWTG...
             No Match      1086.2 1399.6 2424.7 2930.3 3086.3 5423.0

        43 : YEX0_YEAST     3.609e+03 64793.9    0.250
             HYPOTHETICAL 64.8 KDA PROTEIN IN GDI1-COX15 INTERGENIC REGION.
             Mw     Start  End    Seq
             2930.5 328    355    STLSIVINILCGPMVSVVGSEVLVDWAK
             5423.5 223    271    CLLVSMSLTYVTIHGYVLVYQAISLNIAVNSYSNALLTLLLSMQF...
             No Match      1086.2 1399.6 2030.2 2424.7 3086.3 6082.8

        44 : Y323_MYCPN     3.263e+03 25772.7    0.250
             HYPOTHETICAL PROTEIN MG323 HOMOLOG.
             Mw     Start  End    Seq
             1398.6 171    182    EHTNANLISIMR
             5426.1 39     89     TNTAAQEFDHVVCCDGSNLTALAELQLEEFSAVIVGVTNIEASIM...
             No Match      1086.2 2030.2 2424.7 2930.3 3086.3 6082.8

        45 : VP42_ROTS1     3.237e+03 86774.3    0.375
             OUTER CAPSID PROTEIN VP4 (HEMAGGLUTININ) (OUTER LAYER PROTEIN VP4) [CONTAINS: OUTER CAPSID PROTEINS VP5 AND VP8] (VERSION 2).
             Mw     Start  End    Seq
             2030.2 648    666    STQISPNTIPDIVTEASEK
             2931.2 186    210    TAHYSTTNYDSVNMTAFCDFYIIPR
            *6077.9 370    427    SLAANLNSVMCTGGSYNFSLPVGQWPVLTGGAVSLHSAGVTLSTQ...
             No Match      1086.2 1399.6 2424.7 3086.3 5423.0

        46 : NOEC_AZOCA     3.086e+03 33615.6    0.250
             NODULATION PROTEIN NOEC.
             Mw     Start  End    Seq
             1400.7 27     39     NGLLFVPVLICGR
             6081.1 204    260    GYELSDHSIVALICVSAGYAAVVFLELFVQMSSVAQGPAPIFVSN...
             No Match      1086.2 2030.2 2424.7 2930.3 3086.3 5423.0

        47 : BIB_DROME      3.070e+03 76951.0    0.375
             NEUROGENIC PROTEIN BIG BRAIN.
             Mw     Start  End    Seq
             2425.5 570    593    GQSAQSDDSSYGSYHGSAVTPPAR
             2932.4 214    241    FMGNSAASIGCAYSACCFVSMPYLNPAR
            *6083.5 316    375    YQQSQGTYPRGQSNGNGGGQAAGNGQHQAANMGQMPGVVANAGQG...
             No Match      1086.2 1399.6 2030.2 3086.3 5423.0

        48 : NB35_YEAST     3.035e+03 35253.1    0.500
             NBP35 PROTEIN.
             Mw     Start  End    Seq
            *1398.7 281    293    FLGSVPLDPRIGK
             2031.2 56     74     GPDPDIPLITDNLSGIEHK
            *2931.3 48     74     EICESLPKGPDPDIPLITDNLSGIEHK
             3087.4 294    322    SCDMGESFLDNYPDSPASSAVLNVVEALR
             No Match      1086.2 2424.7 5423.0 6082.8

        49 : HSCA_RICPR     2.923e+03 66019.3    0.375
             CHAPERONE PROTEIN HSCA HOMOLOG.
             Mw     Start  End    Seq
            *1399.6 549    560    DAVQTRDQILIK
             2028.3 467    484    ISNISHNIEIKPNHGINK
             5426.1 195    244    YLVYDLGGGTFDVSILNIQEGIFQVIATNGDNMLGGDDIDVVITQ...
             No Match      1086.2 2424.7 2930.3 3086.3 6082.8

        50 : SYL_AERPE      2.902e+03 110518.7   0.500
             LEUCYL-TRNA SYNTHETASE (EC 6.1.1.4) (LEUCINE--TRNA LIGASE) (LEURS).
             Mw     Start  End    Seq
             1085.3 476    484    MEFLPGHVR
             2928.3 770    795    FIEVQTLLIAPFAPHTAEEAWEAMGR
            *3084.5 769    795    RFIEVQTLLIAPFAPHTAEEAWEAMGR
             5419.0 214    261    DGLVYPALTYRPETVFGVTNLWVHPDATYLVAEVDGEERWIIGEQ...
             No Match      1399.6 2030.2 2424.7 6082.8

        Data files

    emowse reads in the pre-computed "Frequencies" data file
    'Efreqs.dat', (See the section "emowse Scoring scheme", above for
    a description of the frequency scores.)

        Notes

    None.

        References

    The paper describing the original 'MOWSE' program is:

    D.J.C.  Pappin, P.  Hojrup and A.J.  Bleasby 'Rapid Identification of
    Proteins by Peptide-Mass Fingerprinting'.  Current Biology (1993), vol
    3, 327-332.

    General references

    Barber M, Bordoli RS, Sedgwick RD, Tyler AN: Fast atom
    bombardment of solids: a new ion source for mass spectrometry. J
    Chem Soc Chem Commun 1981, 7: 325-327.

    Dole M, Mack LL, Hines RL, Mobley RC, Ferguson LD, Alice MB:
    Molecular beams of macroions. J Chem Phys 1968, 49:2240-2249.

    Meng CK, Mann M, Fenn JB: Of protons or proteins.  Z Phys D
    1988, 10: 361-368.

    Karas M, Hillenkamp F: Laser desorption ionisation of proteins
    with molecular masses exceeding 10,000 Daltons. Analytical
    Chemistry 1988, 60:2299-2301.

    Morris H, Panico M, Taylor GW: FAB-mapping of recombinant-DNA
    protein products. Biochem Biophys Res Commun 1983, 117:299-305.

    Morris H, Greer FM: Mass spectrometry of natural and
    recombinant proteins and glycoproteins. Trends in Biotechnology
    1988, 6:140-147.

    Weissenbach J, Gyapay G, Dib C, Vignal J, Morissette J,
    Millasseau P, Vaysseix G, Lathrop M: A second generation linkage
    map of the human genome. Nature 1992, 359:794-801.

    Adams MD, Kelley JM, Gocayne JD, Dubnick M, Polymeropoulos MH,
    Xiao H, Merril CR, Wu A, Olde B, Moreno RF, Kerlavage AR, McCombie
    WR, Venter JC: Complementary DNA sequencing: expressed sequence
    tags and human genome project. Science 1991, 252:1651-1656.

    Lehrach H, Drmanac R, Hoheisel J, Larin Z, Lennon G, Monaco AP,
    Nizetic D, Zehetner G, Poustka A: Hybridization fingerprinting in
    genome mapping and sequencing. In Genome Analysis Volume 1:
    Genetic and Physical Mapping. Cold Spring Harbor Laboratory Press;
    1990:39-81 .

    Akrigg D, Bleasby AJ, Dix NIM, Findlay JBC, North ACT, Parry-
    Smith D, Wootton JC, Blundell TI, Gardner SP, Hayes F, Sternberg
    MJE, Thornton JM, Tickle IJ, Murray-Rust P: A protein
    sequence/structure database. Nature 1988, 335:745-746.

    Bleasby AJ, Wootton JC: Construction of validated, non-
    redundant composite protein databases. Protein Engineering 1990,
    3:153-159.

        Warnings

    None.

        Diagnostic Error Messages

    None.

        Exit status

    It always exits with status 0.

        Known bugs

    None.

    See also

    Program nameDescription
    backtranseqBack translate a protein sequence
    chargeProtein charge plot
    checktransReports STOP codons and ORF statistics of a protein sequence
    compseqCounts the composition of dimer/trimer/etc words in a sequence
    freakResidue/base frequency table or plot
    iepCalculates the isoelectric point of a protein
    mwfilterFilter noisy molwts from mass spec output
    octanolDisplays protein hydropathy
    pepinfoPlots simple amino acid properties in parallel
    pepstatsProtein statistics
    pepwindowDisplays protein hydropathy
    pepwindowallDisplays protein hydropathy of a set of sequences

        Author(s)

    This application was written by Alan Bleasby (ableasby@hgmp.mrc.ac.uk)

        History

    Written (Sept 2000) - author.

        Target users

    This program is intended to be used by everyone and everything, from naive users to embedded scripts.

        Comments