would like to extract cds region and concatenate fasta sequences

[sadiexiaoyu]

Hello, everyone,

Could you help me about the following issues?

I got hundreds of candidate genes which I am interested in and I have extracted the corresponding fasta sequences from transcriptome database of other species. And now I would like to only get their cds region and get rid of the UTR region. And afterwards, I would like to concatenate all the fasta sequences for each species. I wonder perl or python might be helpful to do this, but I cannot find the proper answer from the internet or in this forum. Did anyone have the experience?

Thanks in advance!

All the best,

Sadiexiaoyu

[Brian Bushnell]

This sounds a little tricky. Often, I find it useful to concatenate all sequences in a fasta file into a single sequence (normally padded with some number of Ns between the original sequences), so the BBMap package contains fuse.sh for this purpose. But, that assumes you already have the exonic sequence. You'll need to look for another tool to get that...

Note that this is a bit more tricky in the presence of differential splicing, which you obviously have, given that your species has introns. In fact, it might be helpful if you could provide as much information as possible - for example, what species are these? What are you trying to do? What kind of data do you have? Etc.