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JenBarb 12-15-2017 07:51 AM

miRNA seed sequence to target zebrafish genome
Does anyone have any advice on how I can take a 7mer seed sequence of about 500 miRNAs and run a blast on all zebrafish genes in order to find perfect hits throughout the gene (not just in 3' UTR)...
Would like to generate a list of genes for each miRNA of interest that has a perfect alignment with my 7 seed sequence for that miRNA...

Any advice would be great.


GenoMax 12-15-2017 08:06 AM

Cross-posted and answered on BioStars:

JenBarb 12-15-2017 08:10 AM

Thank you. Blast at zfin does not seem to work with such short sequences so i am looking for other options or suggestions to this question.

GenoMax 12-15-2017 08:35 AM

You have to use fuzznuc from EMBOSS. You can use web front end if you are not able to use it on the command line (e.g. ). You may need to do it against individual chromosomes if the web tool does not accept the entire zebrafish genome.

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