
                              EMBOSS: fuzztran
     _________________________________________________________________
   
                               Program fuzztran
                                       
Function

   Protein pattern search after translation
   
Description

   fuzztran uses PROSITE style protein patterns to search nucleic acid
   sequences translated in the specified frame(s).
   
   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.
   
Usage

   Here is a sample session with fuzztran, using all options.

% 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/Spiropl
asma
         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]:
Search pattern: RA
Number of mismatches [0]:
Output file [rnops.fuzztran]:

Command line arguments

   Mandatory qualifiers:
  [-sequence]          seqall     Sequence database USA
   -pattern            string     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
   -mismatch           integer    Number of mismatches
  [-outfile]           report     (no help text) report value

   Optional qualifiers:
   -frame              menu       Frame(s) to translate
   -table              menu       Code to use

   Advanced qualifiers: (none)
   General qualifiers:
  -help                bool       report command line options. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   

   Mandatory qualifiers Allowed values Default
   [-sequence]
   (Parameter 1) Sequence database 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 Any string is accepted An empty string is
   accepted
   -mismatch Number of mismatches Integer 0 or more 0
   [-outfile]
   (Parameter 2) (no help text) report value Report file
   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 qualifiers Allowed values Default
   (none)
   
Input file format

   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).
       
   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://www.uk.embnet.org/Software/EMBOSS/Themes/ReportFormats.html for
   further information on report formats.
   
   By default fuzztran writes a 'table' report file.
   
   The output from the above example is:
   
########################################
# Program: fuzztran
# Rundate: Thu Apr 11 13:46:20 2002
# Report_file: rnops.fuzztran
########################################

#=======================================
#
# Sequence: RNOPS     from: 1   to: 1493
# HitCount: 9
#
# Pattern: RA
# Mismatch: 0
# TransTable: 0
# Frames: F
#
#=======================================

  Start     End   Score Mismatch  Frame PStart   PEnd Translation
     97     102       2        .      1     33     34 RA
    133     138       2        .      1     45     46 RA
    421     426       2        .      1    141    142 RA
    625     630       2        .      1    209    210 RA
    835     840       2        .      1    279    280 RA
    919     924       2        .      1    307    308 RA
    227     232       2        .      2     76     77 RA
    752     757       2        .      2    251    252 RA
     72      77       2        .      3     24     25 RA

#---------------------------------------
#---------------------------------------

Data files

   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:
     * . (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 Mitochondrial
          
   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
          
   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         Protein proteolytic enzyme or reagent cleavage digest
   dreg           regular expression search of a nucleotide sequence
   fuzznuc        Nucleic acid pattern search
   fuzzpro        Protein pattern search
   helixturnhelix Report nucleic acid binding motifs
   marscan        Finds MAR/SAR sites in nucleic sequences
   oddcomp        Finds 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:
   
     * dreg - Regular expression search of a nucleotide sequence
     * preg - Regular expression search of a protein sequence
       
Author(s)

   This application was written by Alan Bleasby (ableasby@hgmp.mrc.ac.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
