Identifying small RNA sequence within whole genome sequence

[Inma]

Hi all,

I want to know if there are any useful bioinformatic tool to find small RNA sequence within a whole bacteria genome.

Thank you in advance,

Inma

[Krish_143]

Hi,
You can use Rfam for predicting the ncRNAs and also check SIPHT.

[Inma]

Hi Krish,

Thank you for your answer. Can I predict small RNA within whole genome using Rfam and SIPHT?
My genome have been sequencing recently, and the functional annotation is not available in any database. Maybe I could search for similar organisms in Pfam, download their small RNA and perform BLAST agaisnt my genome in order to find some of them by similarity. Do you mean that?

Thanks :-)

Inma

[Krish_143]

Hi,

For Identifying ncRNAs,
1) Download directly Rfam database from Rfam.
2) Download Infernal and install it.
using rfam perl script or cmsearch you can find ..

For sRNAs
Use reference

http://newbio.cs.wisc.edu/sRNA/apps/sRNA/submitjob_pegasus_web.php

perform blast and find out it in our genome..

If your interested to use online.. (RNAspace)
* Check with ur genome assembly or use reference and do blast.

For functional annotaion you can use RAST.