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  • How to dig out single particular gene from assembled contigs

    Sorry if this question has been asked before. I just did a RNA-seq of a plant parasitic nematode species, and assembled 50,000 contigs by Trinity.
    I would like to dig out a full-length sequence of endoglucanase gene, and do some protein structure prediction like that. Partial sequence of this gene was available through previous degenerate PCR. Does anybody know a easy and simple way to do it?
    Thanks a lot.

  • #2
    Blast of your Trinity contigs against the partial sequence? Should be fast enough and sensitive enough to pick up the contig(s). Or am I missing something obvious here?

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    • #3
      Originally posted by westerman View Post
      Blast of your Trinity contigs against the partial sequence? Should be fast enough and sensitive enough to pick up the contig(s). Or am I missing something obvious here?
      Hey, Westerman in Purdue, thank you for you replying.
      Are you talking about build a local db or www-blast something like that?

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      • #4
        Local db. Using the older version of blast (although blast+ is similar):

        1) formatdb -i Trinity.fasta -p F -o T
        2) blastall -p blastn -d Trinity.fasta -i myfile.fa -o output.blastn
        3) manually look at output.blastn to figure out the id of the matching contig
        4) fastacmd -d Trinity.fasta -s myid > found.fa

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        • #5
          Thanks westerman -- we modified for the new blast+ as below --

          1) makeblastdb -in Trinity.fasta -dbtype nucl -parse_seqids -out TrinityBlast -title "All contigs"
          2) blastn -query myfile.fa -db TrinityBlast -out myfile.out
          3) same
          4) blastdbcmd -db TrinityBlast -entry myid > found.fa

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