Hi everyone,
I have been working on matching a list of identified mutant sequences from genome sequences against lists of mutant peptides. Frustratingly I have the information, i.e. which genes are mutated and what the changes are, but crucially I need the amino acid sequence of these mutants. I have so far been using the transcript IDs to import the protein sequences of the wild types and then going through and manually making the changes in word. Is there a quick way to get the mutant amino acid sequence? Or even a way to quickly find a specific residue and then change it manually?
Thanks,
Daniel
I think that a tool like ORF finder might be helpfull for you. You can analyze mutant and wildtype sequences and then compare the aminoacid changes in the places where you now there are changes in nucletides
http://www.ncbi.nlm.nih.gov/gorf/gorf.html
Additionally, you would be better off working in a text editor like Textpad (free download) rather than Word. The F8 shortcut enables you to find a stretch of characters in the fasta file and replace the wt sequence with the mutated one. If you have more than a few dozens sequences to deal with, or if you have to re-do this exercise regularly, then it would be advantegeous to automatise the procedure. In Edinburgh, folks in the Genepool facility can probably quickly script sthg under unix to help you: http://genepool.bio.ed.ac.uk/
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