Question: Identifying frame of blast gene fragment
0
gravatar for zgayk
3.5 years ago by
zgayk90
United States
zgayk90 wrote:

Hi,

 

 I want to compare a large list of fragments of gene sequences between two species using dN/dS. The problem is that some of these gene fragments might start with the last nucleotide of a codon rather than a whole codon and the program I am using to compute dN/dS will of course count the reading frame from the gene fragment's first nucleotide even if this is wrong. 

If I had a small number of gene fragments, I could check the fragment frame by hand by downloading the entire gene sequence, finding the start of my fragment in the entire gene, and checking to see if the fragment started with a piece of the prior codon. Then, if the frame was incorrect, I would remove the starting nucleotide from the sequence so that I then had a full codon.

Does anyone know of a way that this could be implemented on a large scale to check ~6,000 gene fragments?

Thank you,

Zach

 

blast sequence gene • 988 views
ADD COMMENTlink modified 3.5 years ago • written 3.5 years ago by zgayk90
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: 1267 users visited in the last hour