ARAMEMNON, a novel database for Arabidopsis integral membrane proteins
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ARAMEMNON, a novel database for Arabidopsis integral membrane proteins. / Schwacke, Rainer; Schneider, Anja; van der Graaff, Eric; Fischer, Karsten Brask; Catoni, Elisabetta; Desimone, Marcelo; Frommer, Wolf B; Flügge, Ulf-Ingo; Kunze, Reinhard.
In: Plant Physiology, Vol. 131, No. 1, 01.2003, p. 16-26.Research output: Contribution to journal › Journal article › Research
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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
VL - 131
SP - 16
EP - 26
JO - Plant Physiology
JF - Plant Physiology
SN - 0032-0889
IS - 1
ER -
ID: 106391501