sirna.ihelp

emboss的linux版本的源代码

   Standard (Mandatory) qualifiers:
  [-sequence]          seqall     Nucleotide sequence(s) filename and optional
                                  format, or reference (input USA)
  [-outfile]           report     [*.sirna] The output is a table of the
                                  forward and reverse parts of the 21 base
                                  siRNA duplex. Both the forward and reverse
                                  sequences are written 5' to 3', ready to be
                                  ordered. The last two bases have been
                                  replaced by 'dTdT'. The starting position of
                                  the 23 base region and the %GC content is
                                  also given. If you wish to see the complete
                                  23 base sequence, then either look at the
                                  sequence in the other output file, or use
                                  the qualifier '-context' which will display
                                  the 23 bases of the forward sequence in this
                                  report withthe first two bases in brackets.
                                  These first two bases do not form part of
                                  the siRNA probe to be ordered.
  [-outseq]            seqoutall  [<sequence>.<format>] This is a file of the
                                  sequences of the 23 base regions that the
                                  siRNAs are selected from. You may use it to
                                  do searches of mRNA databases (e.g. REFSEQ)
                                  to confirm that the probes are unique to the
                                  gene you wish to use it on.

   Additional (Optional) qualifiers:
   -poliii             boolean    [N] This option allows you to select only
                                  the 21 base probes that start with a purine
                                  and so can be expressed from Pol III
                                  expression vectors. This is the NARN(17)YNN
                                  pattern that has been suggested by Tuschl et
                                  al.
   -aa                 boolean    [N] This option allows you to select only
                                  those 23 base regions that start with AA. If
                                  this option is not selected then regions
                                  that start with AA will be favoured by
                                  giving them a higher score, but regions that
                                  do not start with AA will also be reported.
   -tt                 boolean    [N] This option allows you to select only
                                  those 23 base regions that end with TT. If
                                  this option is not selected then regions
                                  that end with TT will be favoured by giving
                                  them a higher score, but regions that do not
                                  end with TT will also be reported.
   -[no]polybase       boolean    [Y] If this option is FALSE then only those
                                  23 base regions that have no repeat of 4 or
                                  more of any bases in a row will be reported.
                                  No regions will ever be reported that have
                                  4 or more G's in a row.
   -context            boolean    [N] The output report file gives the
                                  sequences of the 21 base siRNA regions ready
                                  to be ordered. This does not give you an
                                  indication of the 2 bases before the 21
                                  bases. It is often interesting to see which
                                  of the suggested possible probe regions have
                                  an 'AA' in front of them (i.e. it is useful
                                  to see which of the 23 base regions start
                                  with an 'AA'). This option displays the
                                  whole 23 bases of the region with the first
                                  two bases in brackets, e.g. '(AA)' to give
                                  you some context for the probe region. YOU
                                  SHOULD NOT INCLUDE THE TWO BASES IN BRACKETS
                                  WHEN YOU PLACE AN ORDER FOR THE PROBES.

   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
   -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

   "-outseq" associated qualifiers
   -osformat3          string     Output seq format
   -osextension3       string     File name extension
   -osname3            string     Base file name
   -osdirectory3       string     Output directory
   -osdbname3          string     Database name to add
   -ossingle3          boolean    Separate file for each entry
   -oufo3              string     UFO features
   -offormat3          string     Features format
   -ofname3            string     Features file name
   -ofdirectory3       string     Output directory

   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