Question: a protein failed to be aligned to genome by tblastn
0
gravatar for lin.pei26
3.0 years ago by
lin.pei2670
China
lin.pei2670 wrote:

Hi all:

I have a protein sequence which I know the genomic region where it came from. also I have the CDS.

by blasting the CDS to the genome, I can find the exact position of that transcript. however, the first 200 AA of the protein could not be aligned to the corresponding region by tblastn.

Could any one help me to understand what happened ? Thanks in advance! Best,

blast • 819 views
ADD COMMENTlink modified 3.0 years ago • written 3.0 years ago by lin.pei2670

I think their might be a large intronic region after 200 AA as BLAST looks for local alignment and the region for the 200 AA is little bit far upstream BLAST might have missed it. try tblastn using only the 200 AA and it may give alignment upstrem of your present alignment.

Hope this works.

ADD REPLYlink written 3.0 years ago by gangireddy160

Thanks! I have tried this but found that the first 200 AA could not be aligned to genome by tblastn when using this 200AA as query alone. as a control, another 200AA in the middle of the protein could be aligned to the correct position with a %identity < 60%.

ADD REPLYlink written 3.0 years ago by lin.pei2670
1
gravatar for lin.pei26
3.0 years ago by
lin.pei2670
China
lin.pei2670 wrote:

I solved this problem by turing off two options of tblastn: -seg and -comp_based_stats.

the former was for filtering low-complexity sequence.

[1] http://community.gep.wustl.edu/repository/course_materials_WU/annotation/Annotation_Strategy_Guide.pdf

ADD COMMENTlink modified 3.0 years ago • written 3.0 years ago by lin.pei2670

Is that a "yes", this worked to address your original question?

ADD REPLYlink modified 3.0 years ago • written 3.0 years ago by genomax67k

Thanks. I modify my comment, making it clear enough to follow my original question.

ADD REPLYlink written 3.0 years ago by lin.pei2670

You may also want to accept this answer (use the tick mark) to mark the question as answered.

ADD REPLYlink written 3.0 years ago by genomax67k
0
gravatar for natasha.sernova
3.0 years ago by
natasha.sernova3.4k
natasha.sernova3.4k wrote:

Try tblastx. Usually it is much more successful than tblastn.

ADD COMMENTlink modified 3.0 years ago • written 3.0 years ago by natasha.sernova3.4k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1943 users visited in the last hour