BetaWrap Search Form

Please paste your amino acid sequence(s) in FASTA format below. (Click here for the NCBI's description of FASTA format.)

We ask that you not exceed 500 sequences or 500,000 amino acids. For larger jobs, send email to betawrap@csail.mit.edu -- we'd be glad to run them for you.

If this is your first time using BetaWrap, please take a moment to read our page of advice on using the program.

Advanced Options

Modify Search Parameters:

Turn off filtering for regions of high alpha-helical content.

Ignore residues in the T1 and T3 turns. In the known beta-helix structures, the positions which bound the beta-strands have distinctive characteristics, some of which are incorporated in the algorithm. By ignoring these positions, one can increase the chance of giving a good score to a completely novel structure which doesn't share these features, at the expense of some discrimination between the known structures and non-beta-helices.

Run Additional Searches:

Rung profile search: BetaWrap uses structural features of the known beta-helices to score query sequences. For sequences which have some sequence similarity with the known beta-helices, this HMMER-powered profile search with aligned rungs from known beta-helices may give greater confidence and/or more accurate alignments. Search for rungs. Details here.

Search for other coiled folds: a search with Pfam HMM's for leucine rich repeats and hexapeptide repeats. These folds occasionally score well under the BetaWrap algorithm. Details here.

Thanks to Sean Eddy and the Pfam Consortium for permission to use Pfam HMM's and the HMMER software.