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  • JenBarb
    Member
    • Oct 2010
    • 47
    #1

    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!
    Tags: mirna, seed sequence, zebrafish
  • GenoMax
    Senior Member
    • Feb 2008
    • 7142
    #2
    Cross-posted and answered on BioStars: https://www.biostars.org/p/289409/

    Comment

    • JenBarb
      Member
      • Oct 2010
      • 47
      #3
      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.

      Comment

      • GenoMax
        Senior Member
        • Feb 2008
        • 7142
        #4
        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.

        Comment

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