Conserved regions in multiple fasta files (multiple species)?

Question

[debitboro]

Dear biostars members,

I've multiple fasta files containing a different number of transcripts of different species (one file for each species). I want to find conserved regions in sequences between the species. I'm completely new to this topic. I've performed some search and I found ClustalW is suitable for such purpose. Other people use SEEKR and QuasiAlign. I've installed ClustalW but the command line requires only one input fasta file (-i argument). How can I feed the tool with multiple fasta files ?

Any idea about how to perform that, or can you provide me with tools and/or idea to do that?

Thanks in advance

[Jautis]

Do you want just conserved regions, or gene orthologs? If you're interested in orthologs, you could use blast to find matches between each species and the other fasta files

Answer 1

[lieven.sterck]

yes, indeed, most aligner tools (multiple sequence aligners) will take a single fasta file as input.

So, concatenate all your sequences in a single file but do make sure the naming (fasta-header) of each sequence is informative, eg. use a short species ID in it ...