One-Block CYRCA protein-motif search

HELP

[Blocks Home] [Block Searcher][Block Maker] [Get Blocks][Multiple Alignment Processor][Biassed Block Checker]

Note: We found that this site works propertly for Netscape, Firefox (for UNIX, MAC & PC) or Explorer (for PC) web browsers.

A typical search against the Blocks or Prints Database will take 15-60 minutes or more, depending on the number of query blocks and the load on our server. If you choose not to receive the results via email, please be patient.

Enter your email address if you want the results through email:

Please, enter multiple sequence alignment. Your multiple alignment may include up to 400 sequences in one of the following formats: Ungapped regions of at least 10 and at most 55 amino acids will be carved out of the submitted multiple alignment and converted to Blocks format. Use Multiple Alignment Processor for other parameters. You can insert a column of gaps in your FASTA, CLUSTAL or MSF alignment to force block edges. If you want to keep a gapped columns, replace all gap characters in it with Xs (unknown aa character).
Parameters:
Use these defaults or enter other values.

minimum Z-score

Linear Edge Score

A search may take 15-60 minutes: Please be patient.

[LAMA Searcher Help] [Blocks Home] [Block Searcher][Block Maker] [Get Blocks][Multiple Alignment Processor][Biassed Block Checker]

[CYRCA algorithm]

CYRCA paper: Kunin V, Chan B, Sitbon E, Lithwick G, Pietrokovski S, Consistency analysis of similarity between multiple alignments: prediction of protein function and fold structure from analysis of local sequence motifs. J Mol Biol. 2001 Mar 30;307(3):939-49.
Mail Milana Frenkel-Morgenstern.