Protein homolog query issue
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12 weeks ago
jaqx008 ▴ 110

Hello all,

I am trying to find protein/nucleotide sequence homolog of one species (A.0) in a related species (A.1). The gene in A.0 has been well annotated and deposited in ncbi. Genes in A.1 seem to be very poorly annotated and I can not find them using ncbi blast. I have performed tblastn locally but can not identify the gene when I load a mapped file in IGV because there is no gff file to tell where the gene starts and end in IGV. Is there a way you all can suggest I handle this problem without having to create annotation for the entire A.1?

Also, I plan to find transcript expression levels in transcriptom of A.1. Would it be appropriate to directly use the genes from A.0 to do this? I do not think so but what do you think?

transcriptom blast species sequence Related • 176 views
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If the genome is available but poorly annotated, I don't see how you can avoid getting better annotations. Try with exonerate.

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