EMBOSS: fuzztran

| fuzztran

## 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/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]:

Go to the input files for this example
Go to the output files for this example

## Command line arguments

       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
       -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. 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

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 | (1)
2 | (2)
3 | (3)
F | (Forward three frames)
-1 | (-1)
-2 | (-2)
-3 | (-3)
R | (Reverse three frames)
6 | (All six frames)
| 1
-table | Code to use |
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)
| 0
Advanced (Unprompted) qualifiers | Allowed values | Default
(none)

## Input file format

fuzztran reads in normal nucleic acid sequence USAs.

### 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   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
    //

### 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, 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.

### Output files for usage example

### File: z46957.fuzztran

    ########################################
    # Program: fuzztran
    # Rundate: Tue 15 Jul 2008 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  Strand   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
    #---------------------------------------

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
digest | Reports on protein proteolytic enzyme or reagent cleavage sites
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
helixturnhelix | Identify nucleic acid-binding motifs in protein sequences
marscan | Finds matrix/scaffold recognition (MRS) signatures in DNA sequences
oddcomp | Identify proteins with specified sequence word composition
patmatdb | Searches protein sequences with a sequence motif
patmatmotifs | Scan a protein sequence with motifs from the PROSITE database
pepcoil | Predicts coiled coil regions in protein sequences
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

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:

- dreg - Regular expression search of a nucleotide sequence
- preg - Regular expression search of a protein sequence

## Author(s)

Alan Bleasby (ajb © ebi.ac.uk)
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK

## 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