automatically get description of genes found by blast
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4.4 years ago
dp ▴ 50

Hi I BLASTed genes predicted from metagenomic contigs against nr/nt. For each match I get the accession and coordinates of the match in the reference. How can I programmatically get the annotations of these matches.

For example, if I use the ncbi blast server I can go to each gene with matches, go to the "Alignments" tab and then select the link to GenBank. If the matched region is an annotated gene then the GenBank entry has a field labelled "CDS" which has a sub-field "product" that is annotated with the gene function. How can I get these annotations automatically?

Thanks!!

BLAST gene annotation metagenome • 670 views
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Have you checked outfmt 6 option for BLAST+? This will require you to rerun the blast though not sure if you were referring to parsing existing blast results and then getting descriptions you want.

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