Finds siRNA duplexes in mRNA emboss sirna -sequence $input1 -outfile $ofile1 -outseq $ofile2 -poliii $poliii -aa $aa -tt $tt -polybase $polybase -context $context -rformat2 $out_format1 -osformat3 $out_format2 -auto Sequences Select only the 21 base probes that start with a purine (Pol III expression vectors) No Yes Select only those 23 base regions that start with AA No Yes Select only those 23 base regions that end with TT No Yes Report more than those 23 base regions that have no repeat of 4 or more of any bases in a row Yes No Displays the whole 23 bases of the region with the first two bases in brackets No Yes Output Report File Format Table EMBL GENBANK GFF PIR SwissProt DbMotif Diffseq Excel (tab delimited) FeatTable Motif Regions SeqTable SRS Simple SRS TagSeq Output Sequence File Format FASTA (m) ACeDB (m) ASN.1 (m) Clustal (m) CODATA (m) EMBL (m) Fitch (m) Wisconsin Package GCG 9.x and 10.x (s) GENBANK (m) GFF (m) Hennig86 (m) Intelligenetics (m) Jackknifer (m) Jackknifernon (m) Mega (m) Meganon (m) Wisconsin Package GCG's MSF (m) NBRF (PIR) (m) NCBI style FASTA (m) Nexus/PAUP (m) Nexusnon/PAUPnon (m) PHYLIP interleaved (m) PHYLIP non-interleaved (m) SELEX (m) Staden (s) DNA strider (m) SwisProt entry (m) Plain sequence (s) Treecon (m)

.. class:: warningmark The input dataset needs to be sequences. ----- You can view the original documentation here_. .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/sirna.html