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  • Genome in SRA

    Hi,
    I have to find some members of gene's family, in a genome in SRA format, (http://www.ncbi.nlm.nih.gov/Traces/s...tudy=SRP014648).
    Well I convert this SRA to FastQ (fastq-dump) and then in FASTA,
    I decided not assembly because the genome is very hard, and maybe assembly sequences from 2 or more member in one contig (because this family is a little conserved).
    So I compared this genome (in fasta) against my set of genes (all the same family) (blast)
    For my gene1 I had N1 hits, for my gene2 N2 hits... for gene17 I had N17 hits.
    The problem is here, when I compared the hits, most of hits are shared.
    So I can't recognize my genes.

    What do you recommend me?

    Thanks

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