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¶
-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 The last two bases have been replaced by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
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.
