[Bioperl-l] align and profile_align

Liu Haifeng lhaifeng at dso.org.sg
Mon Feb 16 22:14:19 EST 2004


Anybody can help me understand the difference between the methods "align"
and "profile_align" when using Bio::Tools::Run::Alignment::Clustalw to align
multiple protein sequences?

If I have 5 protein sequences, would the 2 options below be same?
1. align the 5 sequences together
2. align the first 4 sequence, then profile_align the alignment obtained
with the last sequence together

I have tested the two options, the consensus_strings obtained are different.
So can anybody tell me how profile_align can be useful?   It seems that
profile_align may save some computation.


Haifeng Liu

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