Introducing variants in a protein sequence
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amolares • 0
@amolares-13142
Last seen 2.0 years ago

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.

protein structure determinationh varianttools • 451 views
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@herve-pages-1542
Last seen 3 days ago
Seattle, WA, United States

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.

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