different frame between BLAST results and genome browser

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jleatherman
Posts: 2
Joined: Tue Jun 19, 2012 9:26 pm

different frame between BLAST results and genome browser

Post by jleatherman » Tue Sep 24, 2013 5:03 pm

I'm looking at Biarmipes contig 33. The gene Thd1 has different frames between the BLAST results and the open frame in the genome browser.
I watched Wilson's webinar, and I know that this gene Thd1 has seuqencing errors in exon 5.

Here is the summary of exons:
coordinates; Blast frame; frame in genome browser
Exon 1: 16279-14694; -3; -2
Exon 2: 11750-11118; -3; -2
Exon 3: 10,570-10,405 ; -1 ; -3
Exon 4: 10307- 9945 ; -2 ; -1
Exon 5: has sequencing errors, broken into 2 exons
1st block 7116-? ; -3 ; -3
2nd block ?-4561; -1 ; -3

I have checked several things:
1. The sequence on the fasta file we used for BLAST, and the beginning sequence of the fosmid on genome browser start with the same bases.
2. I checked the first exon of another gene on the fosmid, Pur-alpha. For that exon, the frame is right, but the coordinates are off (BLAST exon 1 aligns perfectly, the methionine is at base 25230, but in the genome browser, that same sequence is present, but the methionine is at 25242)

I'm wondering if there was a "fix" done for the sequencing error in Thd1, but it somehow messed things up.
-Judy

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

Re: different frame between BLAST results and genome browser

Post by wleung » Tue Sep 24, 2013 5:43 pm

There were two sequencing errors in Thd1 that have been fixed in the Aug. 2013 assembly. The BLAST results suggests that you might be using the previous version of the assembly which contains the sequencing errors and the frame shifts in the last CDS of Thd1. I just performed the BLASTX alignment of the CDS Thd1:1_1766_0 against the fasta file in the annotation package and the results shows a single contiguous open reading frame (in frame -3) which spans from contig33:4558-7116
Thd1_1_1766_contig33_Dbiarmipes.png
Thd1_1_1766_contig33_Dbiarmipes.png (199.71 KiB) Viewed 5248 times
Consequently, I would like to verify that you are using the sequence from the updated annotation package. The name of the annotation package is dbiarmipes_dot_Aug2013_contig33. If the name of the annotation package is dbiarmipes_dot_Aug2012_contig33.zip, then the sequence is based on the previous assembly which contains two errors in the last CDS of Thd1.

You can download the new contig33 annotation package through the GEP Data Repository (available under the "drosophila_biarmipes/dot_chromosome_v2" section).

I have also checked the links on the production Project Management System and they are all referring to the updated 2013 assemblies. The D. biarmipes projects from 2012 are available through the sandbox Project Management System because some of the curriculum that have been developed last year use projects from that assembly.

jleatherman
Posts: 2
Joined: Tue Jun 19, 2012 9:26 pm

Re: different frame between BLAST results and genome browser

Post by jleatherman » Wed Sep 25, 2013 4:46 pm

Wilson,
I do in fact have the aug2012 version. I will get the updated version, and hopefully that will solve the problems.
Thanks for your help.

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