ARAMEMNON, a novel database for Arabidopsis integral membrane proteins

TY - JOUR

T1 - ARAMEMNON, a novel database for Arabidopsis integral membrane proteins

AU - Schwacke, Rainer

AU - Schneider, Anja

AU - van der Graaff, Eric

AU - Fischer, Karsten Brask

AU - Catoni, Elisabetta

AU - Desimone, Marcelo

AU - Frommer, Wolf B

AU - Flügge, Ulf-Ingo

AU - Kunze, Reinhard

PY - 2003/1

Y1 - 2003/1

N2 - A specialized database (DB) for Arabidopsis membrane proteins, ARAMEMNON, was designed that facilitates the interpretation of gene and protein sequence data by integrating features that are presently only available from individual sources. Using several publicly available prediction programs, putative integral membrane proteins were identified among the approximately 25,500 proteins in the Arabidopsis genome DBs. By averaging the predictions from seven programs, approximately 6,500 proteins were classified as transmembrane (TM) candidate proteins. Some 1,800 of these contain at least four TM spans and are possibly linked to transport functions. The ARAMEMNON DB enables direct comparison of the predictions of seven different TM span computation programs and the predictions of subcellular localization by eight signal peptide recognition programs. A special function displays the proteins related to the query and dynamically generates a protein family structure. As a first set of proteins from other organisms, all of the approximately 700 putative membrane proteins were extracted from the genome of the cyanobacterium Synechocystis sp. and incorporated in the ARAMEMNON DB. The ARAMEMNON DB is accessible at the URL http://aramemnon.botanik.uni-koeln.de.

AB - A specialized database (DB) for Arabidopsis membrane proteins, ARAMEMNON, was designed that facilitates the interpretation of gene and protein sequence data by integrating features that are presently only available from individual sources. Using several publicly available prediction programs, putative integral membrane proteins were identified among the approximately 25,500 proteins in the Arabidopsis genome DBs. By averaging the predictions from seven programs, approximately 6,500 proteins were classified as transmembrane (TM) candidate proteins. Some 1,800 of these contain at least four TM spans and are possibly linked to transport functions. The ARAMEMNON DB enables direct comparison of the predictions of seven different TM span computation programs and the predictions of subcellular localization by eight signal peptide recognition programs. A special function displays the proteins related to the query and dynamically generates a protein family structure. As a first set of proteins from other organisms, all of the approximately 700 putative membrane proteins were extracted from the genome of the cyanobacterium Synechocystis sp. and incorporated in the ARAMEMNON DB. The ARAMEMNON DB is accessible at the URL http://aramemnon.botanik.uni-koeln.de.

KW - Amino Acid Transport Systems

KW - Aquaporins

KW - Arabidopsis

KW - Cluster Analysis

KW - Cyanobacteria

KW - Databases, Protein

KW - Internet

KW - Membrane Proteins

KW - Phylogeny

KW - Protein Sorting Signals

U2 - 10.1104/pp.011577

DO - 10.1104/pp.011577

M3 - Journal article

C2 - 12529511

SN - 0032-0889

VL - 131

SP - 16

EP - 26

JO - Plant Physiology

JF - Plant Physiology

IS - 1

ER -