blast a set of microrna against miRbase microrrna

Question

[najibveto]

hello everyone

i have a set of novel microrna and i want to see if there is homologue microrna from other species especially vertebrate microrna.

can someone tell me which tool to use for doing that? and which protocol to follow?

thanks a lot for your help.

[najibveto]

thanks a lot for your help.

just some question if possible:

• how to get only the vertebrate microrna from mirbase if there is a method?
• how to parse the bowtie aligned file because I didn't work before with bowtie?
• I have the files of my novel microrna as fasta, is it ok to use it as that?
• there is bowtie as external tool in ugene, is it ok to use it?

sorry for the trouble

Answer 1

[BioRyder]

download all known miRNA of vertebrate from miRbase and align with your novel miRNA by using bowtie software. While align with bowtie use mismatch as 1,2 or 3 (-n 1 or -n 2 -n 3). Parse bowtie aligned file and check each novel miRNA aligned is aligned or not, if yes then how many times and its corresponding miRNA id. From these parsed file you can get the information of homologous microRNA.

Answer 2

[Alastair Kerr]

Ensembl have mapped many vertebrate miRNAs and most are cross-referenced to miRbase, Their Biomart system allows per species extraction and their BLAST tool will allow per species sequence searching