                                  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:6.6.0.0

   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
   -scircular1         boolean    Sequence is circular
   -squick1            boolean    Read id and sequence only
   -sformat1           string     Input sequence format
   -iquery1            string     Input query fields or ID list
   -ioffset1           integer    Input start position offset
   -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 INSDC.
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 neighbour 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: Mon 15 Jul 2013 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 Transla
tion
     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        Find antigenic sites in proteins
   dreg             Regular expression search of nucleotide sequence(s)
   epestfind        Find PEST motifs as potential proteolytic cleavage sites
   fuzznuc          Search for patterns in nucleotide sequences
   fuzzpro          Search for patterns in protein sequences
   patmatdb         Search 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            Scan protein sequence(s) with fingerprints from the PRINTS
                    database
   sigcleave        Report 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
