a protein failed to be aligned to genome by tblastn

Question

[Pei]

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,

[gangireddy]

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.

[Pei]

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%.

Answer 1

[Pei]

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

[GenoMax]

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

[Pei]

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

[GenoMax]

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

Answer 2

[natasha.sernova]

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