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HMMER2 Search

user: GUEST

MSA Input Paste a multiple sequence alignment (MSA) in this text area (supported formats) examples multiple FASTA format identifier
This form lets you build a HMMER2 profile-HMM from a multiple sequence alignment (MSA), and search the databases of protein sequences with it. The HMMER2 package was written by Sean Eddy. Only those options that are most useful to build a profile from an MSA are available below. Warning: This service is very computer intensive, please be patient.

Parameters
Database of sequences	ecoli - Escherichia coli K12 proteome sw - Swiss-Prot sw_var - Swiss-Prot splice variants tr - TrEMBL ens - ENSEMBL peptides ur50 - UniRef50 ur50_win20 - UniRef50 window shuffled (w=20)
Taxonomic restriction (NCBI taxonomic browser)	- no restriction [all]- Archaea [taxid:2157] Bacteria (eubacteria) [taxid:2] Eukaryota (eucaryotes) [taxid:2759] Fungi [taxid:4751] Metazoa [taxid:33208] Arthropoda [taxid:6656] Viridiplantae [taxid:33090] Viruses [taxid:10239] Homo_sapiens (human) [taxid:9606] Mus_musculus (house mouse) [taxid:10090] Xenopus (genus) [taxid:8353] Caenorhabditis elegans [taxid:6239] Drosophila_melanogaster (fruit fly) [taxid:7227] Arabidopsis_thaliana (thale cress) [taxid:3702] Saccharomyces cerevisiae [taxid:4932] Schizosaccharomyces pombe [taxid:4896]
Search method	local on query (fs mode) global on query (ls mode)
E-value inclusion threshold	1e-16 1e-9 1e-6 1e-5 1e-4 1e-3 0.01 0.1 1
E-value report threshold	1e-6 1e-3 0.01 0.1 1 10
Cluster matches at approx. identity level	100 % (all) 90 % 80 % 70 % 60 % 50 %
Template for features propagation Enter a protein identifier (e.g. sw:DSBA_ECOLI) or a full protein entry in SwissProt format.

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