Remove Noncoding Regions From Cdna Sequences

Question

[Katy]

I am trying to create a cDNA file to calculate Ka/Ks values using PAML. and I am wondering if any of you out there can introduce an automated, quick and reliable method of removing the noncoding regions! clustal does not like stop codons! I appreciate your help :) K

[2184687-1231-83-]

Have you got a template protein for the cDNA?

[Leonor Palmeira]

Where do your cDNA sequences come from? your own sequencing? downloaded from public databases? do you have annotations for these sequences? and which species are they from? If you answer these questions, we might be able to help.

[Katy]

Hi, I don't have a template protein for it...but I can use softwares to translate the sequence. This is how I generated my cDNA: I have Brassica nigra BACS, sequenced them, ran a BLAST analysis against Arabidopsis genome and predicted the genes using GlimmerHMM and training data from arabidopsis...then extracted the mRNA features from the gff file. Is it more clear now?

[Vitis]

you're stuck at the extraction mRNA step or already got them?

[Katy]

I already have them! need to remove the noncoding region away!

[Katy]

I have the mRNA sequences for each gene...now i need to remove the noncoding sequences!

[Vitis]

So you want every sequence to start with ATG and cut off the stop codon? I think you probably need coordinates for the UTRs and stop codons, then use a perl script to feed in the coordinates and sequences to do the trimming.

Answer 1

[Vitis]

Ensembl API to grab only the coding regions? You'll have to write some Perl code to do that. I'm not a good programmer but I'm sure the computational folks here will give you an answer with example code.