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Old 05-03-2011, 09:04 PM   #1
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Default Multiple Alignment software for huge amount of peptide sequences/cysteine framework


Last edited by LucasVS; 04-15-2012 at 11:25 PM.
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Old 05-06-2011, 07:20 AM   #2
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I wouldn't align with Excel .... scripts are very slow in it, and I doubt you'll find a bioinformatician willing to touch it!

Why not try muscle, thats a nice quick bit of software. Perhaps muscle can also align cysteines only, with the gap characters (-) you put in. Otherwise maybe subsitute all other amino acids with a fairly neutral amino acid (perhaps Alanine). You can then see if the alignment is mainly determined by the cysteines.
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Old 05-09-2011, 01:40 AM   #3
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Excel for storing sequence data and/or VBA for scripting is a very bad idea in this context.

Try the following:
Convert your sequences to Fasta format (plain text) and use either Muscle (muscle -maxiters 1 -in your-fasta-file) or Mafft (mafft -auto your-fasta-file)

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Old 03-28-2012, 08:15 PM   #4
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I also suggest Muscle
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