Spurious blastX result

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cjones
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Joined: Sun Feb 04, 2007 10:19 pm
Location: Moravian College, Bethlehem PA
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Spurious blastX result

Post by cjones » Tue Mar 26, 2013 4:24 am

The blastX track for biarmipes contig 49 claims that there is homology to unc-13 (all 6 isoforms) between positions 550 and 600. However, it doesn't match any of the exon sequences for unc-13 in the Gene Record Finder and running blastX with that sequence against Dmel proteins or tblastn with the purported Dbia amino acid sequence against the Dmel genome comes up empty. So where is this supposed blastX homology coming from?
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biarm49.png
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Chris Jones
Assoc. Prof. of Biology
Moravian College
Bethlehem PA

wleung
Posts: 185
Joined: Sun Feb 04, 2007 7:41 pm
Location: Washington University in St. Louis

Re: Spurious blastX result

Post by wleung » Tue Mar 26, 2013 5:20 am

The blastx track on the GEP UCSC Genome Browser shows the blastx alignment of full-length D. melanogaster proteins against the D. biarmipes contig. Some of the blastx alignment blocks might be spurious, particularly when the contig only contain part of the protein.

In this case, contig49 contains only part of the unc-13 gene. Clicking on one of the unc-13-PC hit on the blastx track, we find a small region of sequence similarity between 557-589 of contig49 and 2739-2749 of the unc-13-PC protein.
spurious_blastx_match_unc13-PC.png
spurious_blastx_match_unc13-PC.png (81.16 KiB) Viewed 3646 times
Because the alignment is relatively weak and there is a large part of the protein (i.e. 1679-2738) that is missing between this alignment block and the adjacent alignment block, this alignment block at 557-589 of the query is likely spurious.

Note that the blastx track on the GEP UCSC Genome Browser uses a slightly different set of alignment parameters than NCBI BLAST. Consequently, you might not get the same alignment results if you were to perform the same blastx search using web BLAST interface at NCBI. Please refer to the methods section of the "D. mel Proteins" track for additional details on the alignment parameters used to create the blastx track.

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