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How to pull out protein sequences from from BAM files containing genomic alignments

Hi,

I'm trying to pull out protein sequences from BAM files containing genome alignments. What is the best way to do this? Right now, I have a BAM file containing the neanderthal alignment to the human genome and a fasta file containing the human reference sequence. I wasn't sure whether the next step would be to pull out the neanderthal consensus sequence using SAMtools. If so, where do I go from there, and if that's not the case, what should I do next?

samtools genome alignment sequence gene
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updated by RD • RD • written by julia92796 • julia92796

Thanks, this thread is helpful. I have a list of human proteins, as well as the genes coding for these proteins, and I'm trying to find homologs to the proteins in humanoid species. I suspect that the next step in my process is generating the consensus sequence for the neanderthal genome, but after that, I'm not sure exactly where to proceed.

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written by julia92796 • julia92796

Hey @Julia92796, Were you able to figure it out? I'm curious how you built the consensus sequences and aligned them to human proteins. I noticed a lot of insertions, and the MSA seems to be failing at domain regions.

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written by RD • RD

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