Search zebrafish genes with a miRNA target seed sequence

Question

[barbj]

Hello, Does anyone have any thoughts or suggestions on how I could take about 500 or so miRNA 7 base seed sequences and search within all of the known zebrafish genes for matches, not just the UTR?

Thanks.

Answer 1

[Hussain Ather]

Do you have the sequences that you want to use to search? If so, you can BLAST them against the ZFIN database https://zfin.org

Answer 2

[GenoMax]

With a small search pattern like that you may want to use fuzznuc from EMBOSS.