MOCCA HOME PAGE

Multiple OCCurences analysis

• What Is Mocca?

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.

• Related Publications

• 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]

• Downloading Mocca and related packages

Mocca is a part of the t_coffee Package. Please proceed to the t_coffee home page, download the package, install it and follow the instruction given by the Documentation.

• Using Mocca

• Please see the t_coffee/Mocca Documentation also available in
[pdf].

• Servers

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.

• Bug Reports and mailing list

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 cedric.notredame@gmail.com