Hi:

I need to introduce a few variants in a large protein sequence (http://swissvar.expasy.org/cgi-bin/swissvar/result?global_textfield=CMYA5_HUMAN&findProteins=search) and keep it in FASTA format for further analysis.

And also, due to the sequence is too large, I need to cut it into domains for a better handling.

Which bioconductor packages I can use?

Thank you in advance.

Hi,

Maybe there are some more specialized packages for this but one possibility is to use the general purpose string manipulation facilities from the Biostrings package. A good start would be for you to take a look at ?readAAStringSet (to load the AA sequences from a FASTA file), ?replaceAt (to introduce some variants to the sequences), and ?writeXStringSet (to save the AA sequences to a FASTA file).

Hope this helps,

H.