help with consensus sequence

L.A. Moran lamoran at gpu.utcs.utoronto.ca
Thu Aug 6 09:18:09 EST 1992


In response to a request by Mark Platt here is my suggestion on how to
derive a consensus sequence for his bacterial gene. Mark implies in his
request for help that he wants to use a MAC program to do the alignment.

1. find similar sequences using BLAST of FASTA at GenBank
2. retrieve the sequences
3. align amino acid residues manually using a word processor
4. convert to nucleotide alignment by codons
5. derive a consensus manually taking into account the phylogenetic
   distance between species and ignoring biases such as a large number
   of genes from closely related organisms

In my opinion it is wrong to assume that any computer program can do a
better job than an intelligent human when it comes to multiple sequence
alignments and deriving a consensus.

Laurence A. Moran (Larry)




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