Question: Protein Coding Region Of Reference Assembled Transcript
0
gravatar for The
7.5 years ago by
The160
United States
The160 wrote:

Hello All,

I've got some sequences of RNA transcript made by 454 sequencing and assembled using sequences from a reference genome. I have the sequence of the transcript and the corresponding GenBank ID of the sequence used for its assembly. I don't have access to the assembly data.

How I can predict the protein coding sequence of the transcript ? Do I need to align them to the reference sequence first? Is there any particular protocol that people follow? Are there any software tools for doing this?

In all probability the sequences contain some frame shift errors. So any remedial method is much appreciated.

Many Thanks

translation transcript • 1.5k views
ADD COMMENTlink modified 7.5 years ago • written 7.5 years ago by The160
0
gravatar for Pappu
7.5 years ago by
Pappu1.9k
Pappu1.9k wrote:

For microbial genome glimmer can recognize coding regions. For eukaryotic genome, look at papers on splice site recognition i.e by Gunnar Rätsch.

ADD COMMENTlink written 7.5 years ago by Pappu1.9k
0
gravatar for The
7.5 years ago by
The160
United States
The160 wrote:

Hi, My sequences are of Eukaryotic origin. The assembly was guided by mRNA sequences and not by Genome sequences. Thanks

ADD COMMENTlink written 7.5 years ago by The160
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: 1940 users visited in the last hour