Using Hmmer 3.0 To Search For Domains Containing A Ptm
Hey, thanks in advance for any help. I'm trying to build an HMM from an alignment of sequences that each contain a requisite PTM. Specifically, they contain a hydrophobic x hydrophobic motif that is ~10-20 residues upstream of a phosphorylated serine or threonine. I'm hoping there is someway to designate a specific character to represent a phosphorylated residue (custom alphabet?), so that I can search a database containing proteins annotated with their known phosphorylation sites. Thanks again.
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Can you show a fragment of the MSA? It should be well aligned to create a HMM. Otherwise you have to use a regular expression in Python/Perl to find it out.
Hey, thanks for the response. I don't have the MSA with me right now, but basically the region between the hydrophobic residues and phosphorylation sites are poorly aligned (pretty much anything). I've been working on REs also, so maybe that's the right way to go.