Question: Search zebrafish genes with a miRNA target seed sequence
0
gravatar for barbj
15 months ago by
barbj0
barbj0 wrote:

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.

ADD COMMENTlink modified 15 months ago by genomax63k • written 15 months ago by barbj0
1
gravatar for Hussain Ather
15 months ago by
Hussain Ather910
National Institutes of Health, Bethesda, MD
Hussain Ather910 wrote:

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

ADD COMMENTlink written 15 months ago by Hussain Ather910
0
gravatar for genomax
15 months ago by
genomax63k
United States
genomax63k wrote:

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

ADD COMMENTlink written 15 months ago by genomax63k
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