Links

Seminars and meetings

Spring Meeting 2012

Maps: e.g. Mouse brain

An interactive, genome-wide image database of gene expression in the mouse brain
(don't forget to download and install the Brain Explorer before first use....!)

citation:
E. Lein, M. Hawrylycz, et. al.: Genome-wide atlas of gene expression in the adult mouse brain..
Nature 445, pp. 168 - 176 (2007).

Yeast databases / AAA server

DRYGIN: Data Repository of Yeast Genetic Interactions

DRYGIN is a database of quantitative genetic interactions of S. cerevisiae derived from the SGA double-mutant arrays
conducted in Boone lab at Terrence Donnelly Centre for Cellular and Biochemical Research, University of Toronto.

Judice L.Y. Koh et al. Nucleic Acids Research, 2010, Vol. 38, Database issue D502-D507:
"DRYGIN: a database of quantitative genetic interaction networks in yeast"

Protein complexes in yeast

Gavin et al.: Proteome survey reveals modularity of the yeast cell machinery. Nature (2006).

SCPD - The Promoter Database of Saccharomyces cerevisiae

CYGD / Comprehensive Yeast Genome Database

Incyte: YPD Database.

Saccharomyces Genome Database

Welcome to MIPS / MIPS homepage

MEROPS - The Protease Database

Genomic Expression Programs in the Response of Yeast Cells to Environmental Changes

Web supplement to Gasch et al. (2000) Mol.Biol.Cell 11(12), 4241-4257

MitoP2 - Mitochondrial Proteome Database for yeast and human

Human gene database, with Integrative Annotation Validated by Full-Length cDNA Clones

Predictions of C. elegans Genetic Interactions

W. Zhong and P.W. Sternberg: Genome-Wide Prediction of C. elegans Genetic Interactions.
Science 311, pp. 1481 - 1484 (2006).

Protein analysis: sequences & structures:
Domain searches, BLAST, Prediction of Transmembrane domains etc.

HEFalMp	HEFalMp: a functional map of the human genome. Functional maps offer a way to interactively explore gene, pathway, process, and disease associations predicted from integrating hundreds of publicly available genomic datasets. Curtis Huttenhower et al.. Exploring the human genome with functional maps, Genome Research 2009, PMID 19246570
Prediction of subcellular localisation of proteins	TargetP 1.1	TargetP 1.1 predicts the subcellular location of eukaryotic proteins. The location assignment is based on the predicted presence of any of the N-terminal presequences: chloroplast transit peptide (cTP), mitochondrial targeting peptide (mTP) or secretory pathway signal peptide (SP).
	Predotar	A prediction service for identifying putative N-terminal targeting sequences
	MITOPROT	Prediction of mitochondrial targeting sequences
	WoLF PSORT	Protein Subcellular Localization Prediction
	PsortII	Prediction of protein localization sites in cells
	Mitopred	A genome-scale method for predicting mitochondrial proteins
WWW Interface to Sequence Analysis Software Tools like the Wisconsin Package	restricted access: local / Cologne
EBI	European Bioinformatics Institute
NCBI	National Center for Biotechnology Information
DDBJ	DDBJ (DNA Data Bank of Japan)
The Protein Data Bank	Protein Data Bank Archive of macromolecular structural data
The Predict Protein Server	including direct submission to other prediction servers: Source of servers
ExPASy Proteomics Server	The ExPASy (Expert Protein Analysis System) proteomics server of the Swiss Institute of Bioinformatics (SIB) is dedicated to the analysis of protein sequences and structures as well as 2-D PAGE
Prosite Server (at ExPASy)	Direct access to the Prosite server at ExPASy
Servers dedicated to the prediction of transmembrane regions	DAS-TMfilter server HMMTOP TMHMM SPLIT Pred-TMR2 ConPred II
REBASE: restriction enzymes, methylases, isoschizomers....	The Restriction Enzyme Database
The Protein Domain Database - ProDom	ProDom is a comprehensive set of protein domain families automatically generated from the SWISS-PROT and TrEMBL sequence databases
The NCBI BLAST homepage	The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences.....

Literature / Papers.....

PubMed at the NCBI

ZBMed Cologne: online full-text access to many journals

Universitäts- und Stadtbücherei: online full-text access to many journals