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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 nucleotide sequence(s): tembl:Z46957
Search pattern: RA
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]:
Output report [z46957.fuzztran]:
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Go to the input files for this example
Go to the output files for this example
Standard (Mandatory) qualifiers:
[-sequence] seqall Nucleotide sequence(s) filename and optional
format, or reference (input USA)
-pattern 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
[-outfile] report [*.fuzztran] Output report file name
Additional (Optional) qualifiers:
-frame menu [1] Frame(s) to translate (Values: 1 (1); 2
(2); 3 (3); F (Forward three frames); -1
(-1); -2 (-2); -3 (-3); R (Reverse three
frames); 6 (All six frames))
-table menu [0] Code to use (Values: 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))
Advanced (Unprompted) qualifiers: (none)
Associated qualifiers:
"-sequence" associated qualifiers
-sbegin1 integer Start of each sequence to be used
-send1 integer End of each sequence to be used
-sreverse1 boolean Reverse (if DNA)
-sask1 boolean Ask for begin/end/reverse
-snucleotide1 boolean Sequence is nucleotide
-sprotein1 boolean Sequence is protein
-slower1 boolean Make lower case
-supper1 boolean Make upper case
-sformat1 string Input sequence format
-sdbname1 string Database name
-sid1 string Entryname
-ufo1 string UFO features
-fformat1 string Features format
-fopenfile1 string Features file name
"-pattern" associated qualifiers
-pformat string File format
-pmismatch integer Pattern mismatch
-pname string Pattern base name
"-outfile" associated qualifiers
-rformat2 string Report format
-rname2 string Base file name
-rextension2 string File name extension
-rdirectory2 string Output directory
-raccshow2 boolean Show accession number in the report
-rdesshow2 boolean Show description in the report
-rscoreshow2 boolean Show the score in the report
-rusashow2 boolean Show the full USA in the report
-rmaxall2 integer Maximum total hits to report
-rmaxseq2 integer Maximum hits to report for one sequence
General qualifiers:
-auto boolean Turn off prompts
-stdout boolean Write standard output
-filter boolean Read standard input, write standard output
-options boolean Prompt for standard and additional values
-debug boolean Write debug output to program.dbg
-verbose boolean Report some/full command line options
-help boolean Report command line options. More
information on associated and general
qualifiers can be found with -help -verbose
-warning boolean Report warnings
-error boolean Report errors
-fatal boolean Report fatal errors
-die boolean Report dying program messages
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| Standard (Mandatory) qualifiers | Allowed values | Default | |||||||||||||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| [-sequence] (Parameter 1) |
Nucleotide sequence(s) filename and optional format, or reference (input 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 | Property value(s) | |||||||||||||||||||||||||||||||||||||
| [-outfile] (Parameter 2) |
Output report file name | Report output file | <*>.fuzztran | ||||||||||||||||||||||||||||||||||||
| Additional (Optional) qualifiers | Allowed values | Default | |||||||||||||||||||||||||||||||||||||
| -frame | Frame(s) to translate |
|
1 | ||||||||||||||||||||||||||||||||||||
| -table | Code to use |
|
0 | ||||||||||||||||||||||||||||||||||||
| Advanced (Unprompted) qualifiers | Allowed values | Default | |||||||||||||||||||||||||||||||||||||
| (none) | |||||||||||||||||||||||||||||||||||||||
ID Z46957; SV 1; linear; mRNA; STD; ROD; 1493 BP.
XX
AC Z46957;
XX
DT 20-DEC-1994 (Rel. 42, Created)
DT 18-APR-2005 (Rel. 83, Last updated, Version 9)
XX
DE R.norvegicus mRNA for rhodopsin.
XX
KW rhodopsin.
XX
OS Rattus norvegicus (Norway rat)
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Euarchontoglires; Glires; Rodentia; Sciurognathi; Muroidea;
OC Muridae; Murinae; Rattus.
XX
RN [1]
RP 1-1493
RX DOI; 10.1074/jbc.271.20.11710.
RX PUBMED; 8662634.
RA Huber A., Sander P.H., Paulsen R.;
RT "Phosphorylation of the InaD gene product, a photoreceptor membrane protein
RT required for recovery of visual excitation";
RL J. Biol. Chem. 271(20):11710-11717(1996).
XX
RN [2]
RP 1-1493
RA Huber A.;
RT ;
RL Submitted (20-DEC-1994) to the EMBL/GenBank/DDBJ databases.
RL Huber A., Universitaet Karlsruhe, Zoologie I, Kornblumenstr. 13, 76128
RL Karlsruhe, Germany
XX
DR EMBL-ALIGN; ALIGN_000323.
XX
FH Key Location/Qualifiers
FH
FT source 1..1493
FT /organism="Rattus norvegicus"
FT /strain="Sprague-Dawley"
FT /mol_type="mRNA"
FT /dev_stage="adult"
FT /clone_lib="rat retinal library"
FT /clone="pRO4"
FT /cell_type="rod"
FT /tissue_type="retina"
FT /db_xref="taxon:10116"
FT 5'UTR 1..83
FT CDS 84..1130
FT /product="rhodopsin"
FT /function="phototransduction"
FT /db_xref="GOA:P51489"
FT /db_xref="UniProtKB/Swiss-Prot:P51489"
FT /citation=[1]
FT /protein_id="CAA87081.1"
FT /translation="MNGTEGPNFYVPFSNITGVVRSPFEQPQYYLAEPWQFSMLAAYMF
FT LLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFV
FT FGPTGCNLEGFFATLGGEIGLWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVM
FT ALACAAPPLVGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFC
FT YGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIFFLICWLPYASVAMYIFTHQGS
FT NFGPIFMTLPAFFAKTASIYNPIIYIMMNKQFRNCMLTTLCCGKNPLGDDEASATASKT
FT ETSQVAPA"
FT 3'UTR 1128..1493
XX
SQ Sequence 1493 BP; 309 A; 475 C; 365 G; 344 T; 0 other;
ggagccgtag gtagctgagc tcgccaggca gccttggtct ctgtctacga acagcccgtg 60
gggcagcctc aagggccgca gccatgaacg gcacagaggg ccccaatttt tatgtgccct 120
tctccaacat cacgggcgtg gtgcgcagcc cctttgagca gccgcagtac tacctggcgg 180
agccatggca gttctccatg ctggcagcct acatgttcct gctcatcgtg ctgggcttcc 240
ccatcaactt cctcacgctc tacgtcaccg tacagcacaa gaagctgcgc acaccactca 300
actacatcct gctcaacttg gctgtggctg acctcttcat ggtcttcgga ggattcacca 360
ccaccctcta cacctcactg catggctact ttgtctttgg gcccacaggc tgcaaccttg 420
agggcttctt tgccaccctt ggaggtgaaa tcggcctgtg gtccctggta gtcctggcca 480
ttgagcgcta cgtggtggtc tgcaagccca tgagcaactt ccgctttggg gagaatcatg 540
ccattatggg tgtggccttc acctgggtca tggcgttggc ctgtgctgct cccccactgg 600
ttggctggtc caggtacatc cccgagggca tgcagtgttc atgtgggatt gactactata 660
cactcaagcc tgaggtcaac aatgagtcct tcgtcatcta catgttcgtg gtccacttca 720
ccatccccat gatcgtcatc ttcttctgct acgggcagct ggtcttcacc gtcaaggagg 780
ccgccgccca gcaacaggag tcggctacca ctcagaaggc agagaaggaa gtcacgcgca 840
tggtcatcat catggtcatc ttcttcctga tctgctggct tccctatgcc agtgtggcca 900
tgtacatctt tacccaccag ggctccaact tcggccccat cttcatgacc cttcccgctt 960
tctttgctaa gaccgcctcc atctacaacc caatcatcta catcatgatg aacaagcagt 1020
tccggaactg catgctcacc acgctctgct gcggcaagaa tccactggga gatgatgagg 1080
cctctgccac tgcctccaag acggagacca gccaggtggc tccagcctaa gcctggccag 1140
agactgtggc tgactgtagg agtctcctgt ccccactcac cccagccaca gcccccacca 1200
ggagcagcac ccgttggaat gaggtcatgc aggctccctc agtgttcttt tctttgtttt 1260
taatgaattc atgaaagcaa aatgaggctc cccactcaac agggacagcc tgacaaagga 1320
catccatcca ccaagacccc cagcctggag tccccaattc ccgggggcca gcgggatctg 1380
tacccctccc ctcagcttgt gtctcaggaa catgacaagt gtcccggctt acggctaagt 1440
gtctaggaca gaatggaaca catagtagct gattaataaa tgctacctgg atg 1493
//
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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://emboss.sf.net/docs/themes/ReportFormats.html for further information on report formats.
By default fuzztran writes a 'table' report file.
########################################
# Program: fuzztran
# Rundate: Sun 15 Jul 2007 12:00:00
# Commandline: fuzztran
# -options
# -sequence tembl:Z46957
# -pattern RA
# -frame f
# Report_format: table
# Report_file: z46957.fuzztran
########################################
#=======================================
#
# Sequence: Z46957 from: 1 to: 1493
# HitCount: 9
#
# Pattern_name Mismatch Pattern
# pattern1 0 RA
# TransTable: 0
# Frames: F
#
#=======================================
Start End Score Pattern_name Mismatch Frame PStart PEnd Translation
97 102 2 pattern1 . 1 33 34 RA
133 138 2 pattern1 . 1 45 46 RA
421 426 2 pattern1 . 1 141 142 RA
625 630 2 pattern1 . 1 209 210 RA
835 840 2 pattern1 . 1 279 280 RA
919 924 2 pattern1 . 1 307 308 RA
227 232 2 pattern1 . 2 76 77 RA
752 757 2 pattern1 . 2 251 252 RA
72 77 2 pattern1 . 3 24 25 RA
#---------------------------------------
#---------------------------------------
#---------------------------------------
# Total_sequences: 1
# Total_hitcount: 9
#---------------------------------------
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The columns of data are as follows:
EMBOSS data files are distributed with the application and stored in the standard EMBOSS data directory, which is defined by the EMBOSS environment variable EMBOSS_DATA.
To see the available EMBOSS data files, run:
% embossdata -showall
To fetch one of the data files (for example 'Exxx.dat') into your current directory for you to inspect or modify, run:
% embossdata -fetch -file Exxx.dat
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 |
| epestfind | Finds PEST motifs as potential proteolytic cleavage sites |
| fuzznuc | Nucleic acid pattern search |
| fuzzpro | Protein pattern search |
| helixturnhelix | Report nucleic acid binding motifs |
| marscan | Finds MAR/SAR sites in nucleic sequences |
| oddcomp | Find 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: