Reference "Assigning membrane spanning regions on proteins listed in the Gramene database"

Reference ID

8210

Title

Assigning membrane spanning regions on proteins listed in the Gramene database

Source

Gramene database, 2004, vol. 1, pp. 1-1

Authors (4)

Jaiswal-P	Ren-L
Lincoln-S	McCouch-S

Abstract

In the Gramene database, the transmembrane feature of a protein and its mapping
to the sub-cellular component, membrane (GO:0016020) a cellular component term
from Gene Ontology are based on the suggestions or inferences derived from, (1)
peer reviewed articles referring the respective protein, (2) determined by
sequence similarity (ISS) in the absence of a published article, (3) Prediction
analysis using web based tool TMHMM, available from
http://www.cbs.dtu.dk/services/TMHMM/. Ref: Moller et. al. (2001), Evaluation of
methods for the prediction of membrane spanning regions; Bioinformatics, 2001,
vol.17, pp646-653. In the electronic/computational prediction methods, the only
default value considered for assigning the Gene Ontoloy term mapping was that
there should be at least two or more number of predicted transmembrane domains.
The associations to GO term carry with them evidences listed either in the
Gramene literature database or hyper linked to an external source. The
associated reference is supported with an evidence code, suggesting the type of
experiment/assertions used in inferring the association. The evidence codes are
listed at http://www.gramene.org/plant_ontology/evidence_codes.html. The
transmembrane feature is always attributed with the start and stop positions of
the transmembrane region in a protein molecule.