Mocca is a repeat extractor. Given one or more sequences, and the approximate position of one of the repeats, Mocca will make it possible to extract all the other occurences and to test seamlessly for new bounds. Mocca will then generate a LOCAL multiple alignment with each sequence fragment identified by its coordinates.
Mocca: semi-automatic method for domain hunting Bioinformatics Vol 17,2001 [pdf]
T-Coffee: A novel method for multiple sequence alignments.
C.Notredame, D. Higgins, J. Heringa,Journal of Molecular Biology,Vol 30 pp205-217,2000[pdf]
COFFEE: A New Objective Function For Multiple Sequence Alignmnent.
C. Notredame, L. Holme and D.G. Higgins,Bioinformatics,Vol 14 (5) 407-422,1998[pdf]
There is currently no mocca server up and running but I will be happy to help setting one up. If you wish to create a mocca server, please inform me and I will link your server to this page.
Mocca is a new method and feed back is very important. If appropriate, a mailing list will be maintained here. Please send me an Email if you wish to make a request or a comment firstname.lastname@example.org