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  • Contigs_Genes_deNovo assembly

    Hello Everyone, I need have a set of contigs from de-novo assembly and would like to find the genes from the set of contigs and match them to a reference sequence.

    If there are large amount of contigs, I think BLAST does not work. Do any of you have tools to suggest me please?

    Thank you.

  • #2
    BLAST does work with a large amount of contigs. It will just take a long time to process

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    • #3
      you may wish to use a genome annotation pipeline such as MAKER (http://www.yandell-lab.org/software/maker.html) to annotate the genes in your contigs. if you have too many contigs i.e. too fragmented assembly, you may not have the complete gene models, however, this would be good starting point.

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