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 The last two bases have been
           replaced by 'dTdT'.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.