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)
