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Old 12-15-2017, 08:51 AM   #1
JenBarb
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Default miRNA seed sequence to target zebrafish genome

Hello,
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.

Thanks!
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Old 12-15-2017, 09:06 AM   #2
GenoMax
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Cross-posted and answered on BioStars: https://www.biostars.org/p/289409/
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Old 12-15-2017, 09:10 AM   #3
JenBarb
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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.
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Old 12-15-2017, 09:35 AM   #4
GenoMax
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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. http://emboss.bioinformatics.nl/cgi-bin/emboss/fuzznuc ). You may need to do it against individual chromosomes if the web tool does not accept the entire zebrafish genome.
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