how to filter rRNA, tRNA, snRNA, snoRNA using Rfam

Question

[manoharankumar01]

Hi,

downloading ftp://ftp.ebi.ac.uk/pub/databases/Rfam/CURRENT/Rfam.tar.gz file.

Create one Rfam.fasta file from above link.

makeblastdb using Rfam.fasta

blastn srna_reads.fa using Rfam.fasta as Database.

filter reads corresponds to rRNA, tRNA, snRNA, snoRNA.

Is this a correct way of doing filtering rRNA, tRNA, snRNA, snoRNA reads?

Thanks,

Manoharan

Answer 1

[pengchy]

Hi manoharankumar01,

Based on my test, you should download all the Rfam sequences in fasta format from: ftp://ftp.ebi.ac.uk/pub/databases/Rfam/CURRENT/fasta_files/. And align your clustered unique small RNA sequences to the Rfam sequences using BLAST or BLAT program. All the families information, including the type of the ncRNAs, can be found here: http://rfam.xfam.org/families.

In addition to align unique sequence to Rfam, you also need to align to the Repbase sequences, which can be downloaded here: http://www.girinst.org/server/RepBase/index.php. Hope this could help you.