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This form lets you build a HMMER3 profile-HMM from a multiple sequence alignment (MSA), and search the databases of protein sequences with it.
The HMMER3 package was written by Sean Eddy. Only those options that are most useful to build a profile from an MSA are available below.
Sequence Input

Mandatory parameters
seq_source sw - Swiss-Prot
bact - Some complete proteomes from Bacteria
arch - Some complete proteomes from Archaea
euk - Some complete proteomes from Eukaryota
ur50 - UniRef50
ur50_win20 - UniRef50 window shuffled (w=20)
ecoli - Escherichia coli K12 proteome

This service is very computer intensive, please be patient.