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?