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EMBOSS: fuzztran |
Patterns are specifications of a (typically short) length of sequence to be found. They can specify a search for an exact sequence or they can allow various ambiguities, matches to variable lengths of sequence and repeated subsections of the sequence.
fuzztran intelligently selects the optimum searching algorithm to use, depending on the complexity of the search pattern specified.
% fuzztran -opt
Protein pattern search after translation
Input sequence(s): embl:rnops
Translation frames
1 : 1
2 : 2
3 : 3
F : Forward three frames
-1 : -1
-2 : -2
-3 : -3
R : Reverse three frames
6 : All six frames
Frame(s) to translate [1]: f
Genetic codes
0 : Standard
1 : Standard (with alternative initiation codons)
2 : Vertebrate Mitochondrial
3 : Yeast Mitochondrial
4 : Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplasma
5 : Invertebrate Mitochondrial
6 : Ciliate Macronuclear and Dasycladacean
9 : Echinoderm Mitochondrial
10 : Euplotid Nuclear
11 : Bacterial
12 : Alternative Yeast Nuclear
13 : Ascidian Mitochondrial
14 : Flatworm Mitochondrial
15 : Blepharisma Macronuclear
16 : Chlorophycean Mitochondrial
21 : Trematode Mitochondrial
22 : Scenedesmus obliquus
23 : Thraustochytrium Mitochondrial
Code to use [0]:
Search pattern: RA
Number of mismatches [0]:
Output file [rnops.fuzztran]:
Mandatory qualifiers:
[-sequence] seqall Sequence database USA
-pattern string The standard IUPAC one-letter codes for the
amino acids are used.
The symbol `x' is used for a position where
any amino acid is accepted.
Ambiguities are indicated by listing the
acceptable amino acids for a given position,
between square parentheses `[ ]'. For
example: [ALT] stands for Ala or Leu or Thr.
Ambiguities are also indicated by listing
between a pair of curly brackets `{ }' the
amino acids that are not accepted at a gven
position. For example: {AM} stands for any
amino acid except Ala and Met.
Each element in a pattern is separated from
its neighbor by a `-'. (Optional in
fuzztran)
Repetition of an element of the pattern can
be indicated by following that element with
a numerical value or a numerical range
between parenthesis. Examples: x(3)
corresponds to x-x-x, x(2,4) corresponds to
x-x or x-x-x or x-x-x-x.
When a pattern is restricted to either the
N- or C-terminal of a sequence, that pattern
either starts with a `<' symbol or
respectively ends with a `>' symbol.
A period ends the pattern. (Optional in
fuzztran).
For example, [DE](2)HS{P}X(2)PX(2,4)C
-mismatch integer Number of mismatches
[-outfile] report (no help text) report value
Optional qualifiers:
-frame menu Frame(s) to translate
-table menu Code to use
Advanced qualifiers: (none)
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 | |||||||||||||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| [-sequence] (Parameter 1) |
Sequence database USA | Readable sequence(s) | Required | ||||||||||||||||||||||||||||||||||||
| -pattern | The standard IUPAC one-letter codes for the amino acids are used. The symbol `x' is used for a position where any amino acid is accepted. Ambiguities are indicated by listing the acceptable amino acids for a given position, between square parentheses `[ ]'. For example: [ALT] stands for Ala or Leu or Thr. Ambiguities are also indicated by listing between a pair of curly brackets `{ }' the amino acids that are not accepted at a gven position. For example: {AM} stands for any amino acid except Ala and Met. Each element in a pattern is separated from its neighbor by a `-'. (Optional in fuzztran) Repetition of an element of the pattern can be indicated by following that element with a numerical value or a numerical range between parenthesis. Examples: x(3) corresponds to x-x-x, x(2,4) corresponds to x-x or x-x-x or x-x-x-x. When a pattern is restricted to either the N- or C-terminal of a sequence, that pattern either starts with a `<' symbol or respectively ends with a `>' symbol. A period ends the pattern. (Optional in fuzztran). For example, [DE](2)HS{P}X(2)PX(2,4)C | Any string is accepted | An empty string is accepted | ||||||||||||||||||||||||||||||||||||
| -mismatch | Number of mismatches | Integer 0 or more | 0 | ||||||||||||||||||||||||||||||||||||
| [-outfile] (Parameter 2) |
(no help text) report value | Report file | |||||||||||||||||||||||||||||||||||||
| Optional qualifiers | Allowed values | Default | |||||||||||||||||||||||||||||||||||||
| -frame | Frame(s) to translate |
|
1 | ||||||||||||||||||||||||||||||||||||
| -table | Code to use |
|
0 | ||||||||||||||||||||||||||||||||||||
| Advanced qualifiers | Allowed values | Default | |||||||||||||||||||||||||||||||||||||
| (none) | |||||||||||||||||||||||||||||||||||||||
The PROSITE pattern definition from the PROSITE documentation follows.
For example, you can look for the pattern:
[DE](2)HS{P}X(2)PX(2,4)C
This means: Two Asps or Glus in any order followed by His, Ser, any residue other then Pro, then two of any residue followed by Pro followed by two to four of any residue followed by Cys.
The search is case-independent, so 'AAA' matches 'aaa'.
The output is a standard EMBOSS report file.
The results can be output in one of several styles by using the command-line qualifier -rformat xxx, where 'xxx' is replaced by the name of the required format. The available format names are: embl, genbank, gff, pir, swiss, trace, listfile, dbmotif, diffseq, excel, feattable, motif, regions, seqtable, simple, srs, table, tagseq
See: http://www.uk.embnet.org/Software/EMBOSS/Themes/ReportFormats.html for further information on report formats.
By default fuzztran writes a 'table' report file.
The output from the above example is:
########################################
# Program: fuzztran
# Rundate: Thu Apr 11 13:46:20 2002
# Report_file: rnops.fuzztran
########################################
#=======================================
#
# Sequence: RNOPS from: 1 to: 1493
# HitCount: 9
#
# Pattern: RA
# Mismatch: 0
# TransTable: 0
# Frames: F
#
#=======================================
Start End Score Mismatch Frame PStart PEnd Translation
97 102 2 . 1 33 34 RA
133 138 2 . 1 45 46 RA
421 426 2 . 1 141 142 RA
625 630 2 . 1 209 210 RA
835 840 2 . 1 279 280 RA
919 924 2 . 1 307 308 RA
227 232 2 . 2 76 77 RA
752 757 2 . 2 251 252 RA
72 77 2 . 3 24 25 RA
#---------------------------------------
#---------------------------------------
EMBOSS data files are distributed with the application and stored in the standard EMBOSS data directory, which is defined by EMBOSS environment variable EMBOSS_DATA.
Users can provide their own data files in their own directories. Project specific files can be put in the current directory, or for tidier directory listings in a subdirectory called ".embossdata". Files for all EMBOSS runs can be put in the user's home directory, or again in a subdirectory called ".embossdata".
The directories are searched in the following order:
The Genetic Code data files are based on the NCBI genetic code tables. Their names and descriptions are:
The format of these files is very simple.
It consists of several lines of optional comments, each starting with a '#' character.
These are followed the line: 'Genetic Code [n]', where 'n' is the number of the genetic code file.
This is followed by the description of the code and then by four lines giving the IUPAC one-letter code of the translated amino acid, the start codons (indicdated by an 'M') and the three bases of the codon, lined up one on top of the other.
For example:
------------------------------------------------------------------------------ # Genetic Code Table # # Obtained from: http://www.ncbi.nlm.nih.gov/collab/FT/genetic_codes.html # and: http://www3.ncbi.nlm.nih.gov/htbin-post/Taxonomy/wprintgc?mode=c # # Differs from Genetic Code [1] only in that the initiation sites have been # changed to only 'AUG' Genetic Code [0] Standard AAs = FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG Starts = -----------------------------------M---------------------------- Base1 = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG Base2 = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG Base3 = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG ------------------------------------------------------------------------------
| Program name | Description |
|---|---|
| antigenic | Finds antigenic sites in proteins |
| digest | Protein proteolytic enzyme or reagent cleavage digest |
| dreg | regular expression search of a nucleotide sequence |
| fuzznuc | Nucleic acid pattern search |
| fuzzpro | Protein pattern search |
| helixturnhelix | Report nucleic acid binding motifs |
| marscan | Finds MAR/SAR sites in nucleic sequences |
| oddcomp | Finds protein sequence regions with a biased composition |
| patmatdb | Search a protein sequence with a motif |
| patmatmotifs | Search a PROSITE motif database with a protein sequence |
| pepcoil | Predicts coiled coil regions |
| preg | Regular expression search of a protein sequence |
| pscan | Scans proteins using PRINTS |
| sigcleave | Reports protein signal cleavage sites |
Other EMBOSS programs allow you to search for regular expression patterns but may be less easy for the user who has never used regular expressions before: