NAME

       sirna - Finds siRNA duplexes in mRNA

SYNOPSIS

       sirna -sequence seqall [-poliii boolean] [-aa boolean] [-tt boolean] [-polybase boolean]
             -outfile report -outseq seqoutall [-context boolean]

       sirna -help

DESCRIPTION

       sirna is a command line program from EMBOSS (“the European Molecular Biology Open Software
       Suite”). It is part of the "Nucleic:Functional sites,Nucleic:2D structure" command
       group(s).

OPTIONS

   Input section
       -sequence seqall

   Sequence input options
       -poliii boolean
           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. Default value: N

       -aa boolean
           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.
           Default value: N

       -tt boolean
           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. Default
           value: N

       -polybase boolean
           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. Default value: Y

   Output section
       -outfile report
           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           last two bases have been replaced by 'dTdT'.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 with the first two bases in brackets. These first two bases do not form part of
           the siRNA probe to be ordered.

       -outseq seqoutall
           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.

       -context boolean
           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. Default
           value: N

BUGS

       Bugs can be reported to the Debian Bug Tracking system (http://bugs.debian.org/emboss), or
       directly to the EMBOSS developers
       (http://sourceforge.net/tracker/?group_id=93650&atid=605031).

SEE ALSO

       sirna is fully documented via the tfm(1) system.

AUTHOR

       Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
           Wrote the script used to autogenerate this manual page.

COPYRIGHT

       This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package.
       It can be redistributed under the same terms as EMBOSS itself.