sirnae - Online in the Cloud

PROGRAM:

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last two bases have been replaced by 'dTdT'.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

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