I am trying to annotate the genome of a recently-sequenced primate species. I noticed that the UCSC browser folks have performed a 46-species whole-genome multiple alignment based on hg19, and I'd like to take advantage of that rather than starting a multi-species genome alignment from scratch. Is there a way for me to take my species' genome and align it into the existing 46-species alignment without restarting the whole thing? I am prepared to accept that the result may not be identical to what I would get if I started from scratch. Essentially my input is a set of MAF files (one for each human chromosome) and a fasta file of all the chromosomes and unlocalized scaffolds in my primate species.
You can add sequences to an existing alignment using MAFFT, and they have written out a very good guide for adding sequences to an existing alignment. There is also a server for trying this out, but I'm not sure you can upload all 47 genomes to their server. Note that while this answers part of your question, I'm not sure this is the best tool for whole genome alignments. If MAFFT is not up to the task, you may want to also look into Mauve, MUMmer, or Encredo and Pecan.
Hi, i read the the guides for MAFFT, but it requires the sequences or alignments with fasta format, is it any tool can using the MAF format?
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Hi! I am interested to know how you solved this issue. Thanks!