patmatdb.ihelp

emboss的linux版本的源代码

   Standard (Mandatory) qualifiers:
  [-sequence]          seqall     Protein sequence(s) filename and optional
                                  format, or reference (input USA)
  [-motif]             string     Patterns for patmatdb are based on the
                                  format of pattern used in the PROSITE
                                  database. For example:
                                  '[DE](2)HS{P}X(2)PX(2,4)C' 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'. (Any string of at least 2
                                  characters)
  [-outfile]           report     [*.patmatdb] Output report file name

   Additional (Optional) qualifiers: (none)
   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

   "-outfile" associated qualifiers
   -rformat3           string     Report format
   -rname3             string     Base file name
   -rextension3        string     File name extension
   -rdirectory3        string     Output directory
   -raccshow3          boolean    Show accession number in the report
   -rdesshow3          boolean    Show description in the report
   -rscoreshow3        boolean    Show the score in the report
   -rusashow3          boolean    Show the full USA in the report
   -rmaxall3           integer    Maximum total hits to report
   -rmaxseq3           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