fuzztran Wiki The master copies of EMBOSS documentation are available at http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki. Please help by correcting and extending the Wiki pages. Function Search for patterns in protein sequences (translated) Description fuzztran searches for a specified PROSITE-style pattern in nucleic acid sequences that are first translated to protein in the specified frame(s) with a specified genetic code. Such 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. One or more nucleotide sequences are read from file. The output is a standard EMBOSS report file that includes data such as location and score of any matches. Usage Here is a sample session with fuzztran % fuzztran -opt Search for patterns in protein sequences (translated) 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/Spiropla sma 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]: Go to the input files for this example Go to the output files for this example Command line arguments Search for patterns in protein sequences (translated) Version: EMBOSS:6.4.0.0 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 (default -rformat table) 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 -rstrandshow2 boolean Show the nucleotide strand 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 first file to standard output -filter boolean Read first file from standard input, write first file to 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 and exit. 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 -version boolean Report version number and exit Input file format fuzztran reads in one or more nucleotide sequences. The input is a standard EMBOSS sequence query (also known as a 'USA'). Major sequence database sources defined as standard in EMBOSS installations include srs:embl, srs:uniprot and ensembl Data can also be read from sequence output in any supported format written by an EMBOSS or third-party application. The input format can be specified by using the command-line qualifier -sformat xxx, where 'xxx' is replaced by the name of the required format. The available format names are: gff (gff3), gff2, embl (em), genbank (gb, refseq), ddbj, refseqp, pir (nbrf), swissprot (swiss, sw), dasgff and debug. See: http://emboss.sf.net/docs/themes/SequenceFormats.html for further information on sequence formats. Input files for usage example 'tembl:Z46957' is a sequence entry in the example nucleic acid database 'tembl' Database entry: tembl:Z46957 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 Ensembl-GO; ENSRNOESTG00000823692; Rattus_norvegicus. DR Ensembl-Gn; ENSRNOG00000011144; Rattus_norvegicus. DR Ensembl-TO; ENSRNOESTT00000823692; Rattus_norvegicus. DR Ensembl-Tr; ENSRNOT00000015417; Rattus_norvegicus. DR Ensembl-Tr; ENSRNOT00000064603; Rattus_norvegicus. 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="InterPro:IPR000276" FT /db_xref="InterPro:IPR000732" FT /db_xref="InterPro:IPR001760" FT /db_xref="InterPro:IPR017452" FT /db_xref="InterPro:IPR019477" 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 // Pattern specification Patterns for fuzztran are based on the format of pattern used in the PROSITE database, with the difference that the terminating dot '.' and the hyphens, '-', between the characters are optional. The PROSITE pattern definition from the PROSITE documentation follows. * 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 given 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). * All other characters, including spaces are not allowed. 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'. Output file format 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, dasgff, debug, listfile, dbmotif, diffseq, draw, restrict, excel, feattable, motif, nametable, 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. Output files for usage example File: z46957.fuzztran ######################################## # Program: fuzztran # Rundate: Fri 15 Jul 2011 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 # pattern 0 RA # TransTable: 0 # Frames: F # #======================================= Start End Strand Score Pattern Mismatch Frame PStart PEnd Transl ation 97 102 + 2 pattern: RA . 1 33 34 RA 133 138 + 2 pattern: RA . 1 45 46 RA 421 426 + 2 pattern: RA . 1 141 142 RA 625 630 + 2 pattern: RA . 1 209 210 RA 835 840 + 2 pattern: RA . 1 279 280 RA 919 924 + 2 pattern: RA . 1 307 308 RA 227 232 + 2 pattern: RA . 2 76 77 RA 752 757 + 2 pattern: RA . 2 251 252 RA 72 77 + 2 pattern: RA . 3 24 25 RA #--------------------------------------- #--------------------------------------- #--------------------------------------- # Total_sequences: 1 # Total_length: 1493 # Reported_sequences: 1 # Reported_hitcount: 9 #--------------------------------------- The columns of data are as follows: 1. Start - the start position of the pattern in the nucleic acids sequence. 2. End - the end position of the pattern in the nucleic acids sequence. 3. Score - the score of the match. 4. Mismatch - the number of mismatches . 5. Frame - the translation frame that the pattern match occurs in. 6. PStart - the start position of the match in the resulting protein sequence. 7. PEnd - the end position of the match in the resulting protein sequence. 8. Translation - the protein sequence that is matched. Data files 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: * . (your current directory) * .embossdata (under your current directory) * ~/ (your home directory) * ~/.embossdata The Genetic Code data files are based on the NCBI genetic code tables. Their names and descriptions are: EGC.0 Standard (Differs from GC.1 in that it only has initiation site 'AUG') EGC.1 Standard EGC.2 Vertebrate Mitochodrial EGC.3 Yeast Mitochondrial EGC.4 Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplasma EGC.5 Invertebrate Mitochondrial EGC.6 Ciliate Macronuclear and Dasycladacean EGC.9 Echinoderm Mitochondrial EGC.10 Euplotid Nuclear EGC.11 Bacterial EGC.12 Alternative Yeast Nuclear EGC.13 Ascidian Mitochondrial EGC.14 Flatworm Mitochondrial EGC.15 Blepharisma Macronuclear EGC.16 Chlorophycean Mitochondrial EGC.21 Trematode Mitochondrial EGC.22 Scenedesmus obliquus EGC.23 Thraustochytrium Mitochondrial 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 ------------------------------------------------------------------------------ Notes None. References None. Warnings When translating using non-standard genetic code table, always check the table carefully for deviations from your particular organism's code. Diagnostic Error Messages None. Exit status It always exits with status 0. Known bugs None. See also Program name Description antigenic Finds antigenic sites in proteins dreg Regular expression search of nucleotide sequence(s) epestfind Finds PEST motifs as potential proteolytic cleavage sites fuzznuc Search for patterns in nucleotide sequences fuzzpro Search for patterns in protein sequences patmatdb Searches protein sequences with a sequence motif patmatmotifs Scan a protein sequence with motifs from the PROSITE database preg Regular expression search of protein sequence(s) pscan Scans protein sequence(s) with fingerprints from the PRINTS database sigcleave Reports on signal cleavage sites in a protein sequence Author(s) Alan Bleasby European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK Please report all bugs to the EMBOSS bug team (emboss-bug (c) emboss.open-bio.org) not to the original author. History Written (2000) - Alan Bleasby '-usa' added (13 March 2001) - Gary Williams Target users This program is intended to be used by everyone and everything, from naive users to embedded scripts. Comments None