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  • Find the next best hit

    Hi,
    I am using blast+ for my blast.
    I have created database from a fasta file and and I am blasting the same file against the database created.
    I got the output in tabular format, with Query id, subject id and e-value.

    Most of them would have e-value as 0, (as it is obvious)
    other have output as:

    Q1 Sub1 4e-08
    Q1 Sub2 9e-45

    can I compare 4e-08 and 9e-45 in perl?

    Please help me.
    how do I get the second best hit from this?
    Bioinformaticscally calm

  • #2
    Perl should recognize those as numbers:

    perl -e "if(4e-08 > 9e-45) {print 'Perl can handle scientific notation.'}"

    Are you asking about how to parse the records themselves?

    Comment


    • #3
      @atcghelix
      Thank you.
      I didn't know that Perl can handle scientific notation.
      I was afraid, that Perl might consider these as strings.


      Originally posted by atcghelix View Post
      Perl should recognize those as numbers:

      perl -e "if(4e-08 > 9e-45) {print 'Perl can handle scientific notation.'}"

      Are you asking about how to parse the records themselves?
      Bioinformaticscally calm

      Comment


      • #4
        Maybe:

        Get best hits:

        sort -k1,1 -k3,3g blastOutput | sort -u -k1,1 --merge > bestHits

        Remove best hits from the output:

        grep -v -f bestHits blastOutput > blastOutputBestHitsRemoved

        Get the now best hits:

        sort -k1,1 -k3,3g blastOutputBestHitsRemoved | sort -u -k1,1 --merge > secondBestHits
        savetherhino.org

        Comment

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