runFunCUT

MOBY Web Services (synchronous and asynchronous) that describe the FunCUT method. Is recommended use asynchronous MOBY services because the method needs huge range of time.

FunCUT Method

Short Description: Annotates homologous sequences and includes new features related to the specific identification of protein subfamilies (orthologous groups)

FunCUT (Abascal and Valencia, 2003. PROTEINS: Structure, Function, and Genetics 53:683– 692 (2003)) is application based on the study of the annotations of homologous sequences and includes new features related to the specific identification of protein subfamilies (orthologous groups).

The workflow of the method proceeds as follows:

1. A sequence similitary search is carried out to find proteins related to the query sequence. A clustering algorithm is applied in order to identity closely related sequence groups in the set of similar proteins. More related sequences are more likely to share a common function. In some cases, recursive sequence similitary searches lead to better representation of the related subfamilies, which facilitates the clustering.

2. The local alignments with the closely related proteins clusteres together with the query protein are classified in different categories depending on the extent to which the alignments cover the length of the query and target sequences (alignment categories).

3. Key functional annotations of the corresponding proteins are analyzed, including functional descriptions, enzymatic activity codes, and Swiss-Prot style keywords.

4. The transference of information is carried out starting from the alignment categories with a better coverage. A confidence level is assigned to each one of the annotations. This level is derived from the alignment categories.

The FunCUT results, as we said, includes key functional annotations of the corresponding proteins as the functional descriptions, enzymatic activity codes, and Swiss-Prot style keywords. Also, the results includes the clusters of the query protein and the hits of Blast.

Created by Federico Abascal and Alfonso Valencia.

Mantained by José María Fernández and José Manuel Rodríguez.

http://ubio.bioinfo.cnio.es/biotools/FunCUT