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Odd BLASTp alignment result
| Link to this post | posted 18 Feb, 2016 18:49 | |
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Hi All: In tooling around on our genome just now, I saw something (below) in a BLASTp alignment within DNAM that I've never seen before: PGWRDIVATA GFGRXXXXXX XXXXXXEVTV ASGASHTAQL LVEGDNGINY 201 |||||||||| |||||||||| ||| || ||| |||||||||| |||||||||| 201 PGWRDIVATA GFGRALTALT ITPNAPSVTV ASGASHTAQL LVEGDNGINY 251 TPDCTFESSD PLKASVSAN 251 |||||| ||| | ||+|||+ 251 TPDCTFVSSD PTKATVSAS What do the X's mean? You have to mentally scoot the top line over a few spaces to line it up properly, but even still it's interesting that it recognizes some of the Xs as an identity to the target and some not. I've never seen this before. This is from LilDestine, in the product from the ORF that DNA Master calls starting at bp9002. It's a tail protein according to BLASTp at least. |
| Link to this post | posted 24 Feb, 2016 14:45 | |
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Joseph Ross Hi Joe, Those Xs represent a "region of low complexity". What that basically means is that the amino acids there are quite similar to one another, or there are repetitive patterns, and as such they're bait for lots of meaningless alignments. Here's a link to NCBI's explanation. It's not something you should worry about, though! –Dan |