
                               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.


CAPTION: Prefixes to use with sequence information for
emowse


 Prefix Meaning Example

 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) (CHOND
ROITIN 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); RN
A-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) (RIBONU
CLEOTIDE 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 PATHOLOG
Y 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); RN
A-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.-) (HC
T-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 CHA
NNEL, L TYPE, ALPHA-1 POLYPEPTIDE, ISOFORM 6) (RBE-II) (RBE2) (BRAIN CALCIUM CH
ANNEL 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 CHA
NNEL, 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 RESIST
ANCE 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- DEHYDR
OGENASE (EC 1.1.1.47) (HEXOSE-6-PHOSPHATE DEHYDROGENASE); 6- PHOSPHOGLUCONOLACT
ONASE (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 RESIS
TANCE-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 PROTEI
N 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); ISOMA
LTASE (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) [CO
NTAINS: 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
  
    1. 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.
    2. Dole M, Mack LL, Hines RL, Mobley RC, Ferguson LD, Alice MB:
       Molecular beams of macroions. J Chem Phys 1968, 49:2240-2249.
    3. Meng CK, Mann M, Fenn JB: Of protons or proteins. Z Phys D 1988,
       10: 361-368.
    4. Karas M, Hillenkamp F: Laser desorption ionisation of proteins
       with molecular masses exceeding 10,000 Daltons. Analytical
       Chemistry 1988, 60:2299-2301.
    5. Morris H, Panico M, Taylor GW: FAB-mapping of recombinant-DNA
       protein products. Biochem Biophys Res Commun 1983, 117:299-305.
    6. Morris H, Greer FM: Mass spectrometry of natural and recombinant
       proteins and glycoproteins. Trends in Biotechnology 1988,
       6:140-147.
    7. 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.
    8. 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.
    9. 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 .
   10. 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.
   11. 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 name Description
   backtranseq Back translate a protein sequence
   charge Protein charge plot
   checktrans Reports STOP codons and ORF statistics of a protein
   sequence
   compseq Counts the composition of dimer/trimer/etc words in a sequence
   freak Residue/base frequency table or plot
   iep Calculates the isoelectric point of a protein
   mwfilter Filter noisy molwts from mass spec output
   octanol Displays protein hydropathy
   pepinfo Plots simple amino acid properties in parallel
   pepstats Protein statistics
   pepwindow Displays protein hydropathy
   pepwindowall Displays 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
