How blastn deal with intron and exons?
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2.6 years ago
flogin ▴ 280

So guys, I have a set of genes (GSTEs 1 to 8) from Aedes mosquitoes, on the new assembly L5 (https://www.vectorbase.org/organisms/aedes-aegypti/lvp_agwg/aaegl5) the gene GSTE8 have an 8kbp length intron (https://www.vectorbase.org/Aedes_aegypti_lvpagwg/Transcript/Exons?db=core;g=AAEL007955;r=2:351607324-351616641;t=AAEL007955-RA).

So if I want to identify GSTEs genes in other mosquitoes (e.g. Aedes albopictus) with a command-line BLASTn analysis, is it better use the whole gene (exons and introns) or just the exons regions (extracting all exons and concatenating in a single sequence)?

Best,

blast blastn genomics • 1.2k views
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BLAST as the name indicates does local alignments so it depends on what exactly you want to do. If you want to do end-to-end alignments then you may want to look at other global alignment algorithms.

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I want to identify and recovery all GSTEs genes in other mosquitos, in this way I think that blastn can be used for genes GSTE1-7 (that doesn't present long introns), but for the gene GSTE8 (the unique with intron greater than 1kbp) I have no idea if I can do this with blastn (even with a relaxed gap_extend value).

**And doesn't have much information about this set of genes in this others species, so I don't know if the introns and exons regions show a similar structure..

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