fuzztran.txt

emboss的linux版本的源代码

0
     catccatcca ccaagacccc cagcctggag tccccaattc ccgggggcca gcgggatctg      138
0
     tacccctccc ctcagcttgt gtctcaggaa catgacaagt gtcccggctt acggctaagt      144
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     gtctaggaca gaatggaaca catagtagct gattaataaa tgctacctgg atg             149
3
//

  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: rnops.fuzztran

########################################
# Program: fuzztran
# Rundate: Sat 15 Jul 2006 12:00:00
# Commandline: fuzztran
#    -options
#    -sequence tembl:rnops
#    -pattern RA
#    -frame f
# Report_format: table
# Report_file: rnops.fuzztran
########################################

#=======================================
#
# Sequence: RNOPS     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
#---------------------------------------

   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         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:

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

Author(s)

   Alan Bleasby (ajb