runFunCUT

Created: 2008-10-03 10:54:45      Last updated: 2008-10-03 11:49:17

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

Information Preview

Information Run

You do not have permission to run this workflow


Information Workflow Components

You do not have permission to see the internals of this workflow

Information Workflow Type

Taverna 1

Information License

All versions of this Workflow are licensed under:

Information Version 1 (of 1)

Information Credits (1)

(People/Groups)

Information Attributions (0)

(Workflows/Files)

None

Information Tags (4)

Log in to add Tags

Information Shared with Groups (0)

None

Information Featured In Packs (0)

None

Log in to add to one of your Packs

Information Attributed By (0)

(Workflows/Files)

None

Information Favourited By (0)

No one

 

Citations (0)

None


Version History

In chronological order:



Reviews Reviews (0)

No reviews yet

Be the first to review!



Comments Comments (0)

No comments yet

Log in to make a comment




Workflow Other workflows that use similar services (0)

There are no workflows in myExperiment that use similar services to this Workflow.