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-   -   miRNA seed sequence to target zebrafish genome (http://seqanswers.com/forums/showthread.php?t=79629)

JenBarb 12-15-2017 07:51 AM

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!

GenoMax 12-15-2017 08:06 AM

Cross-posted and answered on BioStars: https://www.biostars.org/p/289409/

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. 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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