fuzztran.txt

emboss的linux版本的源代码

                                 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


% fuzztran -opt 
Protein pattern search after translation
Input nucleotide sequence(s): tembl:rnops
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/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]: 
Output report [rnops.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
   -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 standard output
   -filter             boolean    Read standard input, write 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

Input file format

   fuzztran reads in normal nucleic acid sequence USAs.

  Input files for usage example

   'tembl:rnops' is a sequence entry in the example nucleic acid database
   'tembl'

  Database entry: tembl:rnops

ID   RNOPS      standard; RNA; ROD; 1493 BP.
XX
AC   Z46957;
XX
SV   Z46957.1
XX
DT   20-DEC-1994 (Rel. 42, Created)
DT   27-AUG-1996 (Rel. 49, Last updated, Version 8)
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; Rodentia; Sciurognathi; Muridae; Murinae; Rattus.
XX
RN   [1]
RP   1-1493
RA   Huber A., Sander P.H., Paulsen R.;
RT   "Phosphorylation of the InaD gene product, a photoreceptor membrane protei
n
RT   required for recovery of visual excitation";
RL   J. Biol. Chem. 271:11710-11717(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   SWISS-PROT; P51489; OPSD_RAT.
XX
FH   Key             Location/Qualifiers
FH
FT   source          1..1493
FT                   /db_xref="taxon:10116"
FT                   /organism="Rattus norvegicus"
FT                   /strain="Sprague-Dawley"
FT                   /clone="pRO4"
FT                   /dev_stage="adult"
FT                   /tissue_type="retina"
FT                   /cell_type="rod"
FT                   /clone_lib="rat retinal library"
FT   5'UTR           1..83
FT   CDS             84..1130
FT                   /citation=[1]
FT                   /db_xref="SWISS-PROT:P51489"
FT                   /function="phototransduction"
FT                   /product="rhodopsin"
FT                   /protein_id="CAA87081.1"
FT                   /translation="MNGTEGPNFYVPFSNITGVVRSPFEQPQYYLAEPWQFSMLAAYM
F
FT                   LLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYF
V
FT                   FGPTGCNLEGFFATLGGEIGLWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWV
M
FT                   ALACAAPPLVGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFF
C
FT                   YGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIFFLICWLPYASVAMYIFTHQG
S
FT                   NFGPIFMTLPAFFAKTASIYNPIIYIMMNKQFRNCMLTTLCCGKNPLGDDEASATASK
T
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        6
0
     gggcagcctc aagggccgca gccatgaacg gcacagaggg ccccaatttt tatgtgccct       12
0
     tctccaacat cacgggcgtg gtgcgcagcc cctttgagca gccgcagtac tacctggcgg       18
0
     agccatggca gttctccatg ctggcagcct acatgttcct gctcatcgtg ctgggcttcc       24
0
     ccatcaactt cctcacgctc tacgtcaccg tacagcacaa gaagctgcgc acaccactca       30
0
     actacatcct gctcaacttg gctgtggctg acctcttcat ggtcttcgga ggattcacca       36
0
     ccaccctcta cacctcactg catggctact ttgtctttgg gcccacaggc tgcaaccttg       42
0
     agggcttctt tgccaccctt ggaggtgaaa tcggcctgtg gtccctggta gtcctggcca       48
0
     ttgagcgcta cgtggtggtc tgcaagccca tgagcaactt ccgctttggg gagaatcatg       54
0
     ccattatggg tgtggccttc acctgggtca tggcgttggc ctgtgctgct cccccactgg       60
0
     ttggctggtc caggtacatc cccgagggca tgcagtgttc atgtgggatt gactactata       66
0
     cactcaagcc tgaggtcaac aatgagtcct tcgtcatcta catgttcgtg gtccacttca       72
0
     ccatccccat gatcgtcatc ttcttctgct acgggcagct ggtcttcacc gtcaaggagg       78
0
     ccgccgccca gcaacaggag tcggctacca ctcagaaggc agagaaggaa gtcacgcgca       84
0
     tggtcatcat catggtcatc ttcttcctga tctgctggct tccctatgcc agtgtggcca       90
0
     tgtacatctt tacccaccag ggctccaact tcggccccat cttcatgacc cttcccgctt       96
0
     tctttgctaa gaccgcctcc atctacaacc caatcatcta catcatgatg aacaagcagt      102
0
     tccggaactg catgctcacc acgctctgct gcggcaagaa tccactggga gatgatgagg      108
0
     cctctgccac tgcctccaag acggagacca gccaggtggc tccagcctaa gcctggccag      114
0
     agactgtggc tgactgtagg agtctcctgt ccccactcac cccagccaca gcccccacca      120
0
     ggagcagcac ccgttggaat gaggtcatgc aggctccctc agtgttcttt tctttgtttt      126
0
     taatgaattc atgaaagcaa aatgaggctc cccactcaac agggacagcc tgacaaagga      132