Question: Search zebrafish genes with a miRNA target seed sequence
0
gravatar for barbj
2.9 years 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 2.9 years ago by genomax91k • written 2.9 years ago by barbj0
1
gravatar for Hussain Ather
2.9 years ago by
Hussain Ather940
National Institutes of Health, Bethesda, MD
Hussain Ather940 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 2.9 years ago by Hussain Ather940
0
gravatar for genomax
2.9 years ago by
genomax91k
United States
genomax91k wrote:

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

ADD COMMENTlink written 2.9 years ago by genomax91k
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