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  • How to compare ESTs with assembled contigs of the genome?

    Hello,

    I'm performing the genome assemlby, and I've already assembled reads into contigs. I want to compare ESTs with those contigs in order to estimate the accuracy of the assembly.

    Could anyone recommend some software to me? At least I want to find how many percentage of those ESTs can math to the contigs.

    Thank you very much!

  • #2
    Originally posted by Godevil View Post
    Hello,

    I'm performing the genome assemlby, and I've already assembled reads into contigs. I want to compare ESTs with those contigs in order to estimate the accuracy of the assembly.

    Could anyone recommend some software to me? At least I want to find how many percentage of those ESTs can math to the contigs.

    Thank you very much!
    Why not just use blast and have a pretty high cut off to assume they matched well?

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    • #3
      You should use standlone NCBI Blast tool for finding the coverage of assembly.

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      • #4
        BLAT aligns RNA to DNA, taking into consideration splicing sites and is significantly faster than BLAST (http://genome.ucsc.edu/FAQ/FAQblat.html).

        I am currently looking to employ BFAST (http://sourceforge.net/apps/mediawik...itle=Main_Page). Seems to have a much better literature associated with it, and is even faster than BLAT

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