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Last Update: February, 28th 2007 |
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For direct access to submenues just click on a topic listed below! | |
| database collection | |
| DNA sequences | |
| functional classification | |
| gene regulation, transcriptional control | |
| literature | |
| metabolism | |
| mutation | |
| organic molecules | |
| prediction | |
| protein sequences | |
| protein structures | |
| RNA sequences | |
| signal transduction | |
| taxonomy | |
| visualization | |
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database collection(back) | |
| Title: | DBCAT INFOBIOGEN |
| Topics: | database collection |
| Category: | database; |
| Topics: | database collection; |
| Title: | HNB (Helmholtz Network for Bioinformatics) |
| Topics: | database collection |
| Category: | bioinformatic service; |
| Text: | provides problem and task oriented approaches to a range of bioinformatics applications |
| Topics: | gene regulation, transcriptional control; signal transduction; metabolism; DNA sequences; protein sequences; protein structures; functional classification; database collection; prediction; visualization; |
| Contact: | torsten.crass@med.uni-goettingen.de |
| Title: | Microarray Facility Page |
| Topics: | database collection |
| Category: | database; |
| Content: | microarray-related pages |
| Topics: | database collection; |
DNA sequences(back) | |
| Title: | BLAST |
| Topics: | DNA sequences |
| Category: | bioinformatic tool; |
| Content: | basic local alignment search tool |
| Text: | fast sequence comparison tool for protein and DNA sequences (basic local alignment search tool); approximates alignments that optimize a measure of local similarity; basic algorithm can be implemented in many variations and contexts including DNA and protein sequence database searches, motif and gene identification searches etc. |
| Topics: | DNA sequences; protein sequences; |
| Title: | BLAST service at the GBF/NGFN |
| Topics: | DNA sequences |
| Content: | sequence alignment |
| Text: | search in the EMBL database by selecting single subgroups, e.g. mouse, plant, procaryotes |
| Topics: | DNA sequences; protein sequences; |
| Contact: | ngfnblast@gbf.de |
| Title: | ClustalW |
| Topics: | DNA sequences |
| Category: | bioinformatic tool; |
| Content: | sequence alignment |
| Text: | generates multiple sequence alignments for DNA or proteins sequences; gives biologically meaningful multiple alignments of divergent sequences; calculates the best match for the selected sequences; evolutionary relationships can be viewed as Cladograms or Phylograms |
| Topics: | DNA sequences; protein sequences; |
| Title: | DDBJ |
| Topics: | DNA sequences |
| Category: | database; |
| Content: | primary nucleotid sequence database |
| Text: | content of DDBJ, Genbank and EBML is equalized regularly |
| Topics: | DNA sequences; |
| Title: | DNAPLOT |
| Topics: | DNA sequences |
| Category: | bioinformatic tool; |
| Content: | sequence alignment of immunoglobulin and HLA genes |
| Topics: | DNA sequences; |
| Contact: | wmueller@gbf.de |
| Title: | EMBL Nucleotide Sequence Database |
| Topics: | DNA sequences |
| Category: | database; |
| Content: | primary nucleotid sequence database |
| Text: | content of DDBJ, Genbank and EBML is equalized regularly |
| Topics: | DNA sequences; |
| Title: | GDB |
| Topics: | DNA sequences |
| Category: | bioinformatic tool; |
| Content: | genome database |
| Topics: | DNA sequences; protein sequences; |
| Contact: | help@gdb.org |
| Title: | Genbank |
| Topics: | DNA sequences |
| Category: | database; |
| Content: | primary nucleotid sequence database |
| Text: | content of DDBJ, Genbank and EBML is equalized regularly |
| Topics: | DNA sequences; |
| Title: | GeneQuiz |
| Topics: | DNA sequences |
| Category: | bioinformatic tool; |
| Content: | automatized analysis of genomes |
| Topics: | DNA sequences; |
| Title: | Genomes OnLine Database |
| Topics: | DNA sequences |
| Category: | database; |
| Topics: | DNA sequences; |
| Title: | HNB (Helmholtz Network for Bioinformatics) |
| Topics: | DNA sequences |
| Category: | bioinformatic service; |
| Text: | provides problem and task oriented approaches to a range of bioinformatics applications |
| Topics: | gene regulation, transcriptional control; signal transduction; metabolism; DNA sequences; protein sequences; protein structures; functional classification; database collection; prediction; visualization; |
| Contact: | torsten.crass@med.uni-goettingen.de |
| Title: | LocusLink |
| Topics: | DNA sequences |
| Category: | database; |
| Content: | curated DNA sequences |
| Text: | web interface to give centrally organized access to curated sequences and information about genetic loci; provides official nomenclature, aliases, sequence accessions, phenotypes, EC numbers, MIM numbers, UniGene clusters, homology, map locations; up to now organizes information on genes for fruit fly, human, mouse, rat and zebrafish |
| Topics: | DNA sequences; |
| Title: | MatInspector |
| Topics: | DNA sequences |
| Category: | bioinformatic tool; |
| Content: | transcription factor binding site prediction |
| Text: | software tool that utilizes weight matrices of DNA-binding sites to predict putative transcription factor binding site in unknown DNA sequences |
| Topics: | gene regulation, transcriptional control; DNA sequences; prediction; |
| Title: | MBGD |
| Topics: | DNA sequences |
| Category: | database; |
| Content: | microbial genome database for comparative analysis |
| Topics: | DNA sequences; |
| Title: | NCBI (archaeal and bacterial genomes) |
| Topics: | DNA sequences |
| Category: | database; |
| Content: | archaeal and bacterial genomes |
| Topics: | DNA sequences; |
| Title: | NRSub |
| Topics: | DNA sequences |
| Category: | database; |
| Content: | non-redundant database for Bacillus subtilis |
| Text: | access the complete genome of Bacillus subtilis including data on gene mapping and codon usag; references to important other databases (SWISS-PROT, ENZYME and HOBACGEN) given |
| Topics: | DNA sequences; |
| Title: | PIR |
| Topics: | DNA sequences |
| Category: | database; |
| Content: | protein information ressource |
| Topics: | DNA sequences; |
| Title: | RefSeq |
| Topics: | DNA sequences |
| Category: | database; |
| Content: | DNA sequence, mRNAs, proteins |
| Text: | provides reference sequence standards for genomes, transcripts and proteins; focussing on human, mouse and rat genomic sequences, mRNAs, and their corresponding proteins |
| Topics: | DNA sequences; RNA sequences; protein sequences; |
| Title: | TIGR database |
| Topics: | DNA sequences |
| Content: | DNA sequences and protein sequences |
| Text: | collection of curated databases containing DNA and protein sequence, gene expression, function, protein family, and taxonomy for prokaryotes, plants and humans |
| Topics: | DNA sequences; protein sequences; |
functional classification(back) | |
| Title: | COG |
| Topics: | functional classification |
| Category: | database; |
| Content: | cluster of orthologous groups |
| Topics: | functional classification; |
| Title: | CYTOMER |
| Topics: | functional classification |
| Category: | database; |
| Content: | ontology of organs, morphological structures, tissues and their developmental stages; available for C. elegans and human sources |
| Text: | database on ontology of organs, morphological structures, tissues (as expression sources) and their developmental stages; available for C. elegans and human |
| Topics: | functional classification; |
| Contact: | ewi@biobase.de |
| Literature: | 1) 12520026 TRANSFAC: transcriptional regulation, from patterns to profiles. Matys V, Fricke E, Geffers R, Gössling E, Haubrock M, Hehl R, Hornischer K, Karas D, Kel AE, Kel-Margoulis OV, Kloos DU, Land S, Lewicki-Potapov B, Michael H, Münch R, Reuter I, Rotert S, Saxel H, Scheer M, Thiele S and Wingender E(2003) Nucleic Acids Res. 31 (1), 374-378 2) 11125113 The TRANSFAC system on gene expression regulation. Wingender E, Chen X, Fricke E, Geffers R, Hehl R, Liebich I, Krull M, Matys V, Michael H, Ohnhäuser R, Pr¨ss M, Schacherer F, Thiele S and Urbach S(2001) Nucleic Acids Res. 29 (1), 281-283 |
| Title: | HNB (Helmholtz Network for Bioinformatics) |
| Topics: | functional classification |
| Category: | bioinformatic service; |
| Text: | provides problem and task oriented approaches to a range of bioinformatics applications |
| Topics: | gene regulation, transcriptional control; signal transduction; metabolism; DNA sequences; protein sequences; protein structures; functional classification; database collection; prediction; visualization; |
| Contact: | torsten.crass@med.uni-goettingen.de |
gene regulation, transcriptional control(back) | |
| Title: | aMAZE |
| Topics: | gene regulation, transcriptional control |
| Category: | database; |
| Text: | contains data on proteins, genes, compounds, reactions, and information on metabolic pathways from KEGG including a description of a some pathways from E. coli, yeast and human; includes also information on regulation; the author's aim is to create an integrated database including metabolic, regulatory and signal transduction pathways |
| Topics: | gene regulation, transcriptional control; signal transduction; metabolism; |
| Title: | AraC-XylS database |
| Topics: | gene regulation, transcriptional control |
| Category: | database; |
| Topics: | gene regulation, transcriptional control; |
| Title: | BioProspector |
| Topics: | gene regulation, transcriptional control |
| Category: | bioinformatic tool; |
| Content: | analysis of co-regulated genes |
| Text: | predicts transcription factor binding sites among upstream sequences from co-regulated genes (e.g. identified by microarray analysis) |
| Topics: | gene regulation, transcriptional control; signal transduction; |
| Title: | DBTBS |
| Topics: | gene regulation, transcriptional control |
| Category: | database; |
| Topics: | gene regulation, transcriptional control; |
| Title: | DPInteract |
| Topics: | gene regulation, transcriptional control |
| Category: | database; |
| Topics: | gene regulation, transcriptional control; |
| Title: | Gene Networks Database |
| Topics: | gene regulation, transcriptional control |
| Category: | database; |
| Topics: | gene regulation, transcriptional control; |
| Title: | HNB (Helmholtz Network for Bioinformatics) |
| Topics: | gene regulation, transcriptional control |
| Category: | bioinformatic service; |
| Text: | provides problem and task oriented approaches to a range of bioinformatics applications |
| Topics: | gene regulation, transcriptional control; signal transduction; metabolism; DNA sequences; protein sequences; protein structures; functional classification; database collection; prediction; visualization; |
| Contact: | torsten.crass@med.uni-goettingen.de |
| Title: | IFTI |
| Topics: | gene regulation, transcriptional control |
| Category: | database; |
| Topics: | gene regulation, transcriptional control; |
| Title: | MatInspector |
| Topics: | gene regulation, transcriptional control |
| Category: | bioinformatic tool; |
| Content: | transcription factor binding site prediction |
| Text: | software tool that utilizes weight matrices of DNA-binding sites to predict putative transcription factor binding site in unknown DNA sequences |
| Topics: | gene regulation, transcriptional control; DNA sequences; prediction; |
| Title: | PathoDB |
| Topics: | gene regulation, transcriptional control |
| Category: | database; |
| Content: | pathologically relevant mutations in transcription regulating elements |
| Text: | database that contains pathologically relevant mutations in eukaryotic transcription regulating elements and transcription factors |
| Topics: | gene regulation, transcriptional control; |
| Contact: | ewi@biobase.de |
| Literature: | 1) 11125113 The TRANSFAC system on gene expression regulation. Wingender E, Chen X, Fricke E, Geffers R, Hehl R, Liebich I, Krull M, Matys V, Michael H, Ohnhäuser R, Pr¨ss M, Schacherer F, Thiele S and Urbach S(2001) Nucleic Acids Res. 29 (1), 281-283 |
| Title: | PLACE |
| Topics: | gene regulation, transcriptional control |
| Category: | database; |
| Content: | plant cis-acting regulatory DNA elements |
| Topics: | gene regulation, transcriptional control; |
| Title: | PRODORIC |
| Topics: | gene regulation, transcriptional control |
| Category: | database; bioinformatic tool; |
| Content: | bacterial transcription factors and their binding site, genomes, genes, operons, promoters, motifs |
| Text: | PRODORIC is a comprehensive database on transriptional regulation in prokaryotes, focussing data about transcriptional regulators and their corresponding binding sites. In addition to several search options it offers a variety of tools: e.g. genome browser, a visualization tool for functional genomic regions (promoters, operons), weight matrix search for finding potential DNA binding sites |
| Topics: | gene regulation, transcriptional control; signal transduction; metabolism; prediction; |
| Contact: | r.muench@tu-bs.de |
| Literature: | 1) 12519998 PRODORIC: prokaryotic database of gene regulation. Münch R, Hiller K, Barg H, Heldt D, Linz S, Wingender E and Jahn D(2003) Nucleic Acids Res. 31 (1), 266-269 2) 16109747 Virtual Footprint and PRODORIC: an integrative framework for regulon prediction in prokaryotes. Münch R, Hiller K, Grote A, Scheer M, Klein J, Schobert M and Jahn D(2005) Bioinformatics 21 (22), 4187-4189 |
| Title: | PromEC |
| Topics: | gene regulation, transcriptional control |
| Category: | database; |
| Topics: | gene regulation, transcriptional control; |
| Title: | Regulon DB |
| Topics: | gene regulation, transcriptional control |
| Category: | database; |
| Topics: | gene regulation, transcriptional control; |
| Title: | RSA tools |
| Topics: | gene regulation, transcriptional control |
| Category: | bioinformatic tool; |
| Content: | regulatory sequence analysis |
| Text: | contains several software tools designed for the detection of regulatory signals in intergenic sequences; supports all sequenced bacterial genomes and selected eukaryotic genomes of model organisms (e.g. Saccharomyces cerevisiae, Drosophila melanogaster, Caenorhabditis elegans, Arabidopsis thaliana) |
| Topics: | gene regulation, transcriptional control; prediction; |
| Contact: | jvanheld@ucmb.ulb.ac.be |
| Title: | S/MARt DB |
| Topics: | gene regulation, transcriptional control |
| Category: | database; |
| Content: | scaffold/ matrix attached regions of eukaryotic genomes |
| Text: | database that contains scaffold/ matrix attached regions of eukaryotic genomes |
| Topics: | gene regulation, transcriptional control; |
| Contact: | ewi@biobase.de |
| Literature: | 1) 11752340 S/MARt DB: a database on scaffold/matrix attached regions. Liebich I, Bode J, Frisch M and Wingender E(2002) Nucleic Acids Res. 30 (1), 372-374 |
| Title: | TRANSCompel |
| Topics: | gene regulation, transcriptional control |
| Category: | database; |
| Content: | composite elements of transcriptional regulation |
| Text: | database that contains composite elements of transcriptional regulation |
| Topics: | gene regulation, transcriptional control; |
| Contact: | ewi@biobase.de |
| Literature: | 1) 11752329 TRANSCompel: a database on composite regulatory elements in eukaryotic genes. Kel-Margoulis OV, Kel AE, Reuter I, Deineko IV and Wingender E(2002) Nucleic Acids Res. 30 (1), 332-334 |
| Title: | TRANSFAC |
| Topics: | gene regulation, transcriptional control |
| Category: | database; |
| Text: | database on transcriptional regulation in eukaryotes: The database focusses on data about transcription factors, their target genes and regulatory binding sites using the weight-matrix approach. |
| Topics: | gene regulation, transcriptional control; |
| Literature: | 1) 12520026 TRANSFAC: transcriptional regulation, from patterns to profiles. Matys V, Fricke E, Geffers R, Gössling E, Haubrock M, Hehl R, Hornischer K, Karas D, Kel AE, Kel-Margoulis OV, Kloos DU, Land S, Lewicki-Potapov B, Michael H, Münch R, Reuter I, Rotert S, Saxel H, Scheer M, Thiele S and Wingender E(2003) Nucleic Acids Res. 31 (1), 374-378 2) 11125113 The TRANSFAC system on gene expression regulation. Wingender E, Chen X, Fricke E, Geffers R, Hehl R, Liebich I, Krull M, Matys V, Michael H, Ohnhäuser R, Pr¨ss M, Schacherer F, Thiele S and Urbach S(2001) Nucleic Acids Res. 29 (1), 281-283 3) 16381825 TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes. Matys V, Kel-Margoulis OV, Fricke E, Liebich I, Land S, Barre-Dirrie A, Reuter I, Chekmenev D, Krull M, Hornischer K, Voss N, Stegmaier P, Lewicki-Potapov B, Saxel H, Kel AE and Wingender E(2006) Nucleic Acids Res. 34 (Database issue), D108-110 |
| Title: | TRRD |
| Topics: | gene regulation, transcriptional control |
| Category: | database; |
| Content: | transcription regulatory regions database |
| Topics: | gene regulation, transcriptional control; |
literature(back) | |
| Title: | PubMed |
| Topics: | literature |
| Category: | database; |
| Content: | literature database on medical and life science topics |
| Text: | service of the National Library of Medicine; provides access to over 12 million MEDLINE citations (from the mid of 1960's) and publications in life science journals; provides access to numerous sites with full text articles |
| Topics: | literature; |
| Contact: | custserv@nlm.nih.govd |
| Title: | SUBITO |
| Topics: | literature |
| Category: | database; |
| Content: | literature document delivery service (commercial) |
| Text: | provides online investigation capabilities; where available documents can be provided in electronic (e.g. via email) |
| Topics: | literature; |
| Contact: | info@subito-doc.de |
metabolism(back) | |
| Title: | aMAZE |
| Topics: | metabolism |
| Category: | database; |
| Text: | contains data on proteins, genes, compounds, reactions, and information on metabolic pathways from KEGG including a description of a some pathways from E. coli, yeast and human; includes also information on regulation; the author's aim is to create an integrated database including metabolic, regulatory and signal transduction pathways |
| Topics: | gene regulation, transcriptional control; signal transduction; metabolism; |
| Title: | Boehringer Mannheim Biochemical Pathways |
| Topics: | metabolism |
| Category: | database; |
| Topics: | metabolism; |
| Title: | BRENDA |
| Topics: | metabolism |
| Category: | database; |
| Content: | Braunschweig's enzyme database |
| Topics: | metabolism; |
| Title: | EcoCyc |
| Topics: | metabolism |
| Category: | database; |
| Content: | E. coli genes and metabolism |
| Topics: | metabolism; |
| Title: | HNB (Helmholtz Network for Bioinformatics) |
| Topics: | metabolism |
| Category: | bioinformatic service; |
| Text: | provides problem and task oriented approaches to a range of bioinformatics applications |
| Topics: | gene regulation, transcriptional control; signal transduction; metabolism; DNA sequences; protein sequences; protein structures; functional classification; database collection; prediction; visualization; |
| Contact: | torsten.crass@med.uni-goettingen.de |
| Title: | KEGG |
| Topics: | metabolism |
| Category: | database; |
| Content: | Kyoto encyclopedia of genes and genomes |
| Topics: | signal transduction; metabolism; |
| Title: | MetaCyc |
| Topics: | metabolism |
| Category: | database; |
| Content: | metabolic encyclopedia |
| Topics: | metabolism; |
| Title: | PathDB |
| Topics: | metabolism |
| Category: | database; |
| Topics: | metabolism; |
| Title: | PRODORIC |
| Topics: | metabolism |
| Category: | database; bioinformatic tool; |
| Content: | bacterial transcription factors and their binding site, genomes, genes, operons, promoters, motifs |
| Text: | PRODORIC is a comprehensive database on transriptional regulation in prokaryotes, focussing data about transcriptional regulators and their corresponding binding sites. In addition to several search options it offers a variety of tools: e.g. genome browser, a visualization tool for functional genomic regions (promoters, operons), weight matrix search for finding potential DNA binding sites |
| Topics: | gene regulation, transcriptional control; signal transduction; metabolism; prediction; |
| Contact: | r.muench@tu-bs.de |
| Literature: | 1) 12519998 PRODORIC: prokaryotic database of gene regulation. Münch R, Hiller K, Barg H, Heldt D, Linz S, Wingender E and Jahn D(2003) Nucleic Acids Res. 31 (1), 266-269 2) 16109747 Virtual Footprint and PRODORIC: an integrative framework for regulon prediction in prokaryotes. Münch R, Hiller K, Grote A, Scheer M, Klein J, Schobert M and Jahn D(2005) Bioinformatics 21 (22), 4187-4189 |
| Title: | UM-BBD |
| Topics: | metabolism |
| Category: | database; |
| Content: | microbial biocatalysis/biodegradatation |
| Topics: | metabolism; |
| Title: | WIT |
| Topics: | metabolism |
| Category: | database; |
| Content: | interactive metabolic reconstruction |
| Topics: | metabolism; |
mutation(back) | |
| Title: | PMD |
| Topics: | mutation |
| Category: | database; |
| Content: | protein mutant database |
| Text: | covers natural and artificial mutants (random and site-directed ones); does not contain members of the globin and immunoglobulin superfamilies; based on literature |
| Topics: | protein sequences; mutation; |
| Contact: | pmd-admin@pmd.ddbj.nig.ac.jp |
organic molecules(back) | |
| Title: | CSD |
| Topics: | organic molecules |
| Category: | database; |
| Content: | Cambridge structural database |
| Text: | contains structural information about small organic molecules; gives 1D, 2D, and 3D information where known; commercial database that contains more than 250,000 organic compound |
| Topics: | organic molecules; |
prediction(back) | |
| Title: | Cyber-T |
| Topics: | prediction |
| Category: | bioinformatic tool; |
| Text: | Web interface to reliably detect changes in gene expression in large scale gene expression experiments; based on Bayesian statistical approaches |
| Topics: | prediction; |
| Title: | ExPASy Server |
| Topics: | prediction |
| Category: | bioinformatic service; |
| Content: | expert protein analysis system |
| Text: | provides access to several databases and bioinformatic tools covering the analysis of proteins' sequences, structures, and physicochemical parameters (e.g. pI, MW, domain prediction); this service as well as all tools, and databases hosted by the Swiss Institute of Bioinformatics (SIB) |
| Topics: | protein sequences; protein structures; prediction; visualization; |
| Contact: | info@isb-sib.ch |
| Title: | HNB (Helmholtz Network for Bioinformatics) |
| Topics: | prediction |
| Category: | bioinformatic service; |
| Text: | provides problem and task oriented approaches to a range of bioinformatics applications |
| Topics: | gene regulation, transcriptional control; signal transduction; metabolism; DNA sequences; protein sequences; protein structures; functional classification; database collection; prediction; visualization; |
| Contact: | torsten.crass@med.uni-goettingen.de |
| Title: | MatInspector |
| Topics: | prediction |
| Category: | bioinformatic tool; |
| Content: | transcription factor binding site prediction |
| Text: | software tool that utilizes weight matrices of DNA-binding sites to predict putative transcription factor binding site in unknown DNA sequences |
| Topics: | gene regulation, transcriptional control; DNA sequences; prediction; |
| Title: | PRODORIC |
| Topics: | prediction |
| Category: | database; bioinformatic tool; |
| Content: | bacterial transcription factors and their binding site, genomes, genes, operons, promoters, motifs |
| Text: | PRODORIC is a comprehensive database on transriptional regulation in prokaryotes, focussing data about transcriptional regulators and their corresponding binding sites. In addition to several search options it offers a variety of tools: e.g. genome browser, a visualization tool for functional genomic regions (promoters, operons), weight matrix search for finding potential DNA binding sites |
| Topics: | gene regulation, transcriptional control; signal transduction; metabolism; prediction; |
| Contact: | r.muench@tu-bs.de |
| Literature: | 1) 12519998 PRODORIC: prokaryotic database of gene regulation. Münch R, Hiller K, Barg H, Heldt D, Linz S, Wingender E and Jahn D(2003) Nucleic Acids Res. 31 (1), 266-269 2) 16109747 Virtual Footprint and PRODORIC: an integrative framework for regulon prediction in prokaryotes. Münch R, Hiller K, Grote A, Scheer M, Klein J, Schobert M and Jahn D(2005) Bioinformatics 21 (22), 4187-4189 |
| Title: | Promoter Predictor |
| Topics: | prediction |
| Category: | bioinformatic tool; |
| Content: | neural network promoter prediction |
| Topics: | prediction; |
| Title: | RSA tools |
| Topics: | prediction |
| Category: | bioinformatic tool; |
| Content: | regulatory sequence analysis |
| Text: | contains several software tools designed for the detection of regulatory signals in intergenic sequences; supports all sequenced bacterial genomes and selected eukaryotic genomes of model organisms (e.g. Saccharomyces cerevisiae, Drosophila melanogaster, Caenorhabditis elegans, Arabidopsis thaliana) |
| Topics: | gene regulation, transcriptional control; prediction; |
| Contact: | jvanheld@ucmb.ulb.ac.be |
| Title: | SignalP |
| Topics: | prediction |
| Category: | bioinformatic tool; |
| Content: | neural network-based signal peptide prediction |
| Text: | predicts the signal peptides and its cleavage sites in protein sequences; organism range: Gram-positive prokaryotes, Gram-negative prokaryotes, and eukaryotes |
| Topics: | prediction; |
| Title: | TMAP |
| Topics: | prediction |
| Category: | bioinformatic tool; |
| Content: | transmembrane helix prediction |
| Text: | transmembrane detection based on multiple sequence alignment |
| Topics: | prediction; |
protein sequences(back) | |
| Title: | BLAST |
| Topics: | protein sequences |
| Category: | bioinformatic tool; |
| Content: | basic local alignment search tool |
| Text: | fast sequence comparison tool for protein and DNA sequences (basic local alignment search tool); approximates alignments that optimize a measure of local similarity; basic algorithm can be implemented in many variations and contexts including DNA and protein sequence database searches, motif and gene identification searches etc. |
| Topics: | DNA sequences; protein sequences; |
| Title: | BLAST service at the GBF/NGFN |
| Topics: | protein sequences |
| Content: | sequence alignment |
| Text: | search in the EMBL database by selecting single subgroups, e.g. mouse, plant, procaryotes |
| Topics: | DNA sequences; protein sequences; |
| Contact: | ngfnblast@gbf.de |
| Title: | ClustalW |
| Topics: | protein sequences |
| Category: | bioinformatic tool; |
| Content: | sequence alignment |
| Text: | generates multiple sequence alignments for DNA or proteins sequences; gives biologically meaningful multiple alignments of divergent sequences; calculates the best match for the selected sequences; evolutionary relationships can be viewed as Cladograms or Phylograms |
| Topics: | DNA sequences; protein sequences; |
| Title: | ExPASy Server |
| Topics: | protein sequences |
| Category: | bioinformatic service; |
| Content: | expert protein analysis system |
| Text: | provides access to several databases and bioinformatic tools covering the analysis of proteins' sequences, structures, and physicochemical parameters (e.g. pI, MW, domain prediction); this service as well as all tools, and databases hosted by the Swiss Institute of Bioinformatics (SIB) |
| Topics: | protein sequences; protein structures; prediction; visualization; |
| Contact: | info@isb-sib.ch |
| Title: | GDB |
| Topics: | protein sequences |
| Category: | bioinformatic tool; |
| Content: | genome database |
| Topics: | DNA sequences; protein sequences; |
| Contact: | help@gdb.org |
| Title: | HNB (Helmholtz Network for Bioinformatics) |
| Topics: | protein sequences |
| Category: | bioinformatic service; |
| Text: | provides problem and task oriented approaches to a range of bioinformatics applications |
| Topics: | gene regulation, transcriptional control; signal transduction; metabolism; DNA sequences; protein sequences; protein structures; functional classification; database collection; prediction; visualization; |
| Contact: | torsten.crass@med.uni-goettingen.de |
| Title: | JVirGel |
| Topics: | protein sequences |
| Category: | bioinformatic tool; |
| Content: | predicts proteins' mass/pI and visualizes as 2D-gel |
| Text: | JVirGel is a bioinformatic tool that allows to predict the running behavior of proteins utilizing the information contained in their primary structure. The most striking feature is the powerful graphical representation which allows to run a virtual two-dimensional gel of huge amount of proteins simultaneously like whole proteoms. The tool is available as interactive Java applet or HTML map and offers in addition a graphical output of charge curves and hydrophobicity plots. |
| Topics: | protein sequences; |
| Contact: | k.hiller@tu-bs.de |
| Literature: | 1) 12824438 JVirGel: calculation of virtual two-dimensional protein gels. Hiller K, Schobert M, Hundertmark C, Jahn D and Münch R(2003) Nucleic Acids Res. 31 (13), 3862-3865 |
| Title: | PMD |
| Topics: | protein sequences |
| Category: | database; |
| Content: | protein mutant database |
| Text: | covers natural and artificial mutants (random and site-directed ones); does not contain members of the globin and immunoglobulin superfamilies; based on literature |
| Topics: | protein sequences; mutation; |
| Contact: | pmd-admin@pmd.ddbj.nig.ac.jp |
| Title: | RefSeq |
| Topics: | protein sequences |
| Category: | database; |
| Content: | DNA sequence, mRNAs, proteins |
| Text: | provides reference sequence standards for genomes, transcripts and proteins; focussing on human, mouse and rat genomic sequences, mRNAs, and their corresponding proteins |
| Topics: | DNA sequences; RNA sequences; protein sequences; |
| Title: | SWISSPROT |
| Topics: | protein sequences |
| Category: | database; |
| Topics: | protein sequences; |
| Title: | TIGR database |
| Topics: | protein sequences |
| Content: | DNA sequences and protein sequences |
| Text: | collection of curated databases containing DNA and protein sequence, gene expression, function, protein family, and taxonomy for prokaryotes, plants and humans |
| Topics: | DNA sequences; protein sequences; |
protein structures(back) | |
| Title: | ExPASy Server |
| Topics: | protein structures |
| Category: | bioinformatic service; |
| Content: | expert protein analysis system |
| Text: | provides access to several databases and bioinformatic tools covering the analysis of proteins' sequences, structures, and physicochemical parameters (e.g. pI, MW, domain prediction); this service as well as all tools, and databases hosted by the Swiss Institute of Bioinformatics (SIB) |
| Topics: | protein sequences; protein structures; prediction; visualization; |
| Contact: | info@isb-sib.ch |
| Title: | HNB (Helmholtz Network for Bioinformatics) |
| Topics: | protein structures |
| Category: | bioinformatic service; |
| Text: | provides problem and task oriented approaches to a range of bioinformatics applications |
| Topics: | gene regulation, transcriptional control; signal transduction; metabolism; DNA sequences; protein sequences; protein structures; functional classification; database collection; prediction; visualization; |
| Contact: | torsten.crass@med.uni-goettingen.de |
RNA sequences(back) | |
| Title: | RefSeq |
| Topics: | RNA sequences |
| Category: | database; |
| Content: | DNA sequence, mRNAs, proteins |
| Text: | provides reference sequence standards for genomes, transcripts and proteins; focussing on human, mouse and rat genomic sequences, mRNAs, and their corresponding proteins |
| Topics: | DNA sequences; RNA sequences; protein sequences; |
signal transduction(back) | |
| Title: | aMAZE |
| Topics: | signal transduction |
| Category: | database; |
| Text: | contains data on proteins, genes, compounds, reactions, and information on metabolic pathways from KEGG including a description of a some pathways from E. coli, yeast and human; includes also information on regulation; the author's aim is to create an integrated database including metabolic, regulatory and signal transduction pathways |
| Topics: | gene regulation, transcriptional control; signal transduction; metabolism; |
| Title: | BIND |
| Topics: | signal transduction |
| Category: | database; |
| Content: | biomolecular interaction network database |
| Topics: | signal transduction; |
| Title: | Binding Database |
| Topics: | signal transduction |
| Category: | database; |
| Topics: | signal transduction; |
| Title: | Biocarta |
| Topics: | signal transduction |
| Category: | database; |
| Topics: | signal transduction; |
| Title: | BioCyc |
| Topics: | signal transduction |
| Category: | database; |
| Topics: | signal transduction; |
| Title: | BioProspector |
| Topics: | signal transduction |
| Category: | bioinformatic tool; |
| Content: | analysis of co-regulated genes |
| Text: | predicts transcription factor binding sites among upstream sequences from co-regulated genes (e.g. identified by microarray analysis) |
| Topics: | gene regulation, transcriptional control; signal transduction; |
| Title: | COPE (Cytokines Online Pathfinder Encyclopaedia) |
| Topics: | signal transduction |
| Category: | database; |
| Topics: | signal transduction; |
| Title: | CSNDB (Cell Signaling Networks Database) |
| Topics: | signal transduction |
| Category: | database; |
| Topics: | signal transduction; |
| Title: | DIP (Database of Interacting Proteins) |
| Topics: | signal transduction |
| Category: | database; |
| Topics: | signal transduction; |
| Title: | GRID |
| Topics: | signal transduction |
| Category: | database; |
| Content: | general repository for interaction datasets |
| Topics: | signal transduction; |
| Title: | HNB (Helmholtz Network for Bioinformatics) |
| Topics: | signal transduction |
| Category: | bioinformatic service; |
| Text: | provides problem and task oriented approaches to a range of bioinformatics applications |
| Topics: | gene regulation, transcriptional control; signal transduction; metabolism; DNA sequences; protein sequences; protein structures; functional classification; database collection; prediction; visualization; |
| Contact: | torsten.crass@med.uni-goettingen.de |
| Title: | KEGG |
| Topics: | signal transduction |
| Category: | database; |
| Content: | Kyoto encyclopedia of genes and genomes |
| Topics: | signal transduction; metabolism; |
| Title: | MINT |
| Topics: | signal transduction |
| Category: | database; |
| Content: | molecular interaction database |
| Topics: | signal transduction; |
| Title: | NWSTI (New World Science and Technology, Inc.) |
| Topics: | signal transduction |
| Category: | database; |
| Topics: | signal transduction; |
| Title: | PathoPlant |
| Topics: | signal transduction |
| Category: | database; |
| Content: | database on plant-pathogen interactions and pathogenis-related plant signal transduction |
| Text: | PathoPlant is a database on plant-pathogen interactions and components of signal transduction pathways related to plant pathogenesis. The recent focus is the model organism Arabidopsis thaliana. |
| Topics: | signal transduction; |
| Contact: | l.buelow@tu-braunschweig.de. |
| Literature: | 1) 15752070 PathoPlant®: A Database on Plant-Pathogen Interactions. Bülow L, Schindler M, Choi C, and Hehl R (2004) In Silico Biology 4 (), 529-536 |
| Title: | PATIKA |
| Topics: | signal transduction |
| Category: | database; |
| Content: | pathway analysis tool for integration and knowledge acquisition |
| Topics: | signal transduction; |
| Title: | PIM |
| Topics: | signal transduction |
| Category: | database; |
| Topics: | signal transduction; |
| Title: | PRODORIC |
| Topics: | signal transduction |
| Category: | database; bioinformatic tool; |
| Content: | bacterial transcription factors and their binding site, genomes, genes, operons, promoters, motifs |
| Text: | PRODORIC is a comprehensive database on transriptional regulation in prokaryotes, focussing data about transcriptional regulators and their corresponding binding sites. In addition to several search options it offers a variety of tools: e.g. genome browser, a visualization tool for functional genomic regions (promoters, operons), weight matrix search for finding potential DNA binding sites |
| Topics: | gene regulation, transcriptional control; signal transduction; metabolism; prediction; |
| Contact: | r.muench@tu-bs.de |
| Literature: | 1) 12519998 PRODORIC: prokaryotic database of gene regulation. Münch R, Hiller K, Barg H, Heldt D, Linz S, Wingender E and Jahn D(2003) Nucleic Acids Res. 31 (1), 266-269 2) 16109747 Virtual Footprint and PRODORIC: an integrative framework for regulon prediction in prokaryotes. Münch R, Hiller K, Grote A, Scheer M, Klein J, Schobert M and Jahn D(2005) Bioinformatics 21 (22), 4187-4189 |
| Title: | SENTRA |
| Topics: | signal transduction |
| Category: | database; |
| Content: | sensory signal transduction proteins in procaryotes |
| Topics: | signal transduction; |
| Title: | SPAD |
| Topics: | signal transduction |
| Category: | database; |
| Content: | signaling pathway database |
| Topics: | signal transduction; |
| Title: | STKE |
| Topics: | signal transduction |
| Category: | database; |
| Content: | Signal Transduction Knowledge Environment |
| Topics: | signal transduction; |
| Title: | SubtiList |
| Topics: | signal transduction |
| Category: | database; |
| Topics: | signal transduction; |
| Title: | TRANSPATH |
| Topics: | signal transduction |
| Category: | database; |
| Text: | database on signal transduction networks in eukaryotes: The database focusses on data about mammalian organisms and provides links to gene regulation. |
| Topics: | signal transduction; |
| Literature: | 1) 11724734 The TRANSPATH signal transduction database: a knowledge base on signal transduction networks. Schacherer F, Choi C, Götze U, Krull M, Pistor S and Wingender E(2001) Bioinformatics 17 (11), 1053-1057 2) 16381929 TRANSPATH: an information resource for storing and visualizing signaling pathways and their pathological aberrations. Krull M, Pistor S, Voss N, Kel A, Reuter I, Kronenberg D, Michael H, Schwarzer K, Potapov A, Choi C, Kel-Margoulis O and Wingender E(2006) Nucleic Acids Res. 34 (Database issue), D546-D551 |
taxonomy(back) | |
| Title: | NEWT Taxonomy Database (New EBI Web Taxonomy) |
| Topics: | taxonomy |
| Category: | database; |
| Content: | taxonomy data |
| Text: | NEWT is a taxonomy database which integrates taxonomy data compiled in the NCBI database and the Swiss-Prot protein knowledgebase. The entries are named according to Swiss-Prot nomenclature. |
| Topics: | taxonomy; |
| Contact: | Sandrine.Pilbout@isb-sib.ch |
visualization(back) | |
| Title: | ExPASy Server |
| Topics: | visualization |
| Category: | bioinformatic service; |
| Content: | expert protein analysis system |
| Text: | provides access to several databases and bioinformatic tools covering the analysis of proteins' sequences, structures, and physicochemical parameters (e.g. pI, MW, domain prediction); this service as well as all tools, and databases hosted by the Swiss Institute of Bioinformatics (SIB) |
| Topics: | protein sequences; protein structures; prediction; visualization; |
| Contact: | info@isb-sib.ch |
| Title: | HNB (Helmholtz Network for Bioinformatics) |
| Topics: | visualization |
| Category: | bioinformatic service; |
| Text: | provides problem and task oriented approaches to a range of bioinformatics applications |
| Topics: | gene regulation, transcriptional control; signal transduction; metabolism; DNA sequences; protein sequences; protein structures; functional classification; database collection; prediction; visualization; |
| Contact: | torsten.crass@med.uni-goettingen.de |
| Title: | MolScript |
| Topics: | visualization |
| Text: | program for displaying molecular 3D structures of proteins. |
| Topics: | visualization; |
| Title: | Rasmol |
| Topics: | visualization |
| Category: | bioinformatic tool; |
| Content: | molecular visualization software |
| Text: | molecular visualization software for viewing macromolecular structure and its relation to function |
| Topics: | visualization; |
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