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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 Mitochondrail 10 : Euplotid Nuclear 11 : Bacterial 12 : Alternative Yeast Nuclear 13 : Ascidian Mitochondrial 14 : Flatworm Mitochondrial 15 : Blepharisma Macronuclear Genetic code to use [0]: Search pattern: RA Number of mismatches [0]: Output file [rnops.fuzztran]:
Mandatory qualifiers: [-sequence] seqall Sequence database USA -pattern string Search pattern -mismatch integer Number of mismatches [-outf] outfile Output file name Optional qualifiers: -frame list Frame(s) to translate -table list Genetic code to use Advanced qualifiers: -mmshow bool Show mismatches -accshow bool Show accession numbers -descshow bool Show descriptions |
Mandatory qualifiers | Allowed values | Default | |||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
[-sequence] (Parameter 1) |
Sequence database USA | Readable sequence(s) | Required | ||||||||||||||||||||||||||||
-pattern | Search pattern | Any string is accepted | An empty string is accepted | ||||||||||||||||||||||||||||
-mismatch | Number of mismatches | Integer 0 or more | 0 | ||||||||||||||||||||||||||||
[-outf] (Parameter 2) |
Output file name | Output file | <sequence>.fuzztran | ||||||||||||||||||||||||||||
Optional qualifiers | Allowed values | Default | |||||||||||||||||||||||||||||
-frame | Frame(s) to translate |
|
1 | ||||||||||||||||||||||||||||
-table | Genetic code to use |
|
0 | ||||||||||||||||||||||||||||
Advanced qualifiers | Allowed values | Default | |||||||||||||||||||||||||||||
-mmshow | Show mismatches | Yes/No | No | ||||||||||||||||||||||||||||
-accshow | Show accession numbers | Yes/No | No | ||||||||||||||||||||||||||||
-descshow | Show descriptions | Yes/No | No |
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'.
RNOPS 1 97 RA RNOPS 1 133 RA RNOPS 1 421 RA RNOPS 1 625 RA RNOPS 1 835 RA RNOPS 1 919 RA RNOPS 2 227 RA RNOPS 2 752 RA RNOPS 3 72 RA
It is composed of four columns of data.
If the option '-mmshow' is used, then an extra fourth column of data is output indicating how many mismatches there are:
% fuzztran -mmshow -frame 6 Protein pattern search after translation Input sequence(s): embl:rnops Search pattern: TWLWLT Number of mismatches [0]: 2 Output file [rnops.fuzztran]: stdout RNOPS 1 316 0 TWLWLT RNOPS 1 1138 2 QRLWLT
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 |
---|---|
dreg | regular expression search of a nucleotide sequence |
fuzznuc | Nucleic acid pattern search |
fuzzpro | Protein pattern search |
patmatdb | Search a protein sequence with a motif |
patmatmotifs | Search a PROSITE motif database with a protein sequence |
preg | regular expression search of a protein sequence |
pscan | Scans proteins using PRINTS |
tfscan | Scans DNA sequences for transcription factors |
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: