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Tools
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This is a collection of bioinformatic tools and databases that were developed or expanded during the INTERGENOMICS project. They are listed in alphabetical order.
Where a free online version exists direct access is possible by double-clicking on the tool's name. Literature abstracts - if available - can be viewed in the same way by employing the PMID (Pubmed Database Identifier).
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AthaMap
 | AthaMap is both, a database and web tool. As a database it provides a genome-wide map of putative transcription factor binding sites in Arabidopsis thaliana. As a web tool it enables database-assisted identification of combinatorial cis-regulatory elements and the display of highly conserved transcription factor binding sites.
It contains more than 7.4 million putative binding sites for 36 transcription factors (TFs) from 16 different TF families. A newly implemented functionality allows the display of subsets of higher conserved transcription factor binding sites. Literature:
PMID: 14681436
AthaMap, an online resource for in silico transcription factor binding sites in the Arabidopsis thaliana genome.
Steffens NO, Galuschka C, Schindler M, Bülow L and Hehl R (2004)
Nucleic Acids Res. 32 (Database issue), D368-D372
PMID: 15980498
AthaMap web tools for database-assisted identification of
combinatorial cis-regulatory elements and the display of highly
conserved transcription factor binding sites in Arabidopsis thaliana.
Steffens NO, Galuschka C, Schindler M, Bülow L and Hehl R
(2005)
Nucleic Acids Res. 33 (Web Server issue), W397-W402
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CYTOMER
 | database on ontology of organs, morphological structures, tissues (as expression sources) and their developmental stages; available for C. elegans and human Literature:
PMID: 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
PMID: 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
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JCat
 | JCat (Java Codon Adaptation Tool) provides a novel method for the adaptation of target gene codon usage to most sequenced prokaryotes and selected eukaryotic gene expression hosts. It was developed in order to improve heterologous protein production. In contrast to existing tools, JCat does not require the manual definition of highly expressed genes and is, therefore, a very rapid and easy method.
JCat is integrated into the PRODORIC database that hosts all required information on the various organisms to fulfill the requested calculations. Literature:
PMID: 15980527
JCat: a novel tool to adapt codon usage of a target gene to its potential expression host.
Grote A, Hiller K, Scheer M, Münch R, Nörtemann B, Hempel DC and Jahn D (2005)
Nucleic Acids Res. 33 (Web Server issue), W526-W531
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JProGO
 | JProGO (Java Tool for the Functional Analysis of Prokaryotic Mircorarray Data using the Gene Ontology) is a novel, online accessible program suite for the automatic function interpretation of high-thorughput gene expression data. It identifies Gene Ontology (GO) nodes the expression profile of the genes assigned to which differs significantly from that of the remaining genes highlighting functions and process which play an important role under the investigated condition. In total four statistical methods are offered for the determination of significant GO nodes wich are either threshold-value based (Fisher's exact test) or threshold-value independent (Kolmogorov-Smirnov test, Student's t-test, unpaired Wilcoxon's test). JProGO enables the analysis of microarray expression data from more than 20 different specie, including all important model organisms. Additional features are the recognition of alternative gene names, the correction for multiple testing (FDR method) and the visualization of obtained results both as table and as interactive GO subgraph.
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JVirGel
 | 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. Literature:
PMID: 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
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MineBlast
 | MineBlast is a web service for literature search and presentation based on data-mining results received from UniProt. Users can submit a simple list of protein sequences via a web-based interface. MineBlast performs a BLASTP search in UniProt to identify names and synonyms based on homologous proteins and subsequently queries PubMed, using combined search terms inorder to find and present relevant literature. Literature:
PMID: 15941742
MineBlast: a literature presentation service supporting protein annotation by data mining of BLAST results.
Dieterich G, Kärst U, Wehland J and Jänsch L
(2005)
Bioinformatics 21 (16), 3450-3451
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PathoDB
 | database that contains pathologically relevant mutations in eukaryotic transcription regulating elements and transcription factors Literature:
PMID: 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
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PathoPlant
 | 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. Literature:
PMID: 15752070
PathoPlant®: A Database on Plant-Pathogen Interactions.
Bülow L, Schindler M, Choi C, and Hehl R
(2004)
In Silico Biology 4 (), 529-536
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Phylogenetic Footprint
 | The provided tools allow to transform several types of gene identifiers
(LocusLink, RefSeq, SWISS-PROT, HUGO) to Ensembl gene identifier, which are
used to retrieve upstream sequences. For human, mouse or rat sequences the
corresponding orthologous sequences can be retrieved automatically. The
obtained orthologous sequence pairs are then processed for the detection of
phylogenetic footprints.
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PrediSi
 | PrediSi (Prediction of Signal peptides) is a tool for predicting signal peptide sequences and their cleavage positions in bacterial and eukaryotic amino acid sequences. In contrast to other prediction tools, it is especially useful for the analysis of large datasets - for example whole proteomes - in real time with high accuracy. The method employed is based on a position weight matrix approach improved by a frequency correction which takes in to consideration the amino acid bias present in proteins. Literature:
PMID: 15215414
PrediSi: prediction of signal peptides and their cleavage positions.
Hiller K, Grote G, Scheer M, Münch R and Jahn D
(2004)
Nucleic Acids Res. 32 (Web Server issue), W375-W379
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PRODORIC
 | 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 Literature:
PMID: 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
PMID: 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
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S/MARt DB
 | database that contains scaffold/ matrix attached regions of eukaryotic genomes
Literature:
PMID: 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
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SYSTOMONAS
| SYSTOMONAS is a comprehensive database of molecular networks in Pseudomonas focussing on the organism Pseudomonas aeruginosa. The name SYSTOMONAS is derived from SYSTems Biology of PseudOMONAS. SYSTOMONAS includes systems biology data from transcriptomics, proteomics data, metabolomics as well as sequence data, gene-regulatory networks and biochemical data.
It is a joint project of the Technical University Braunschweig and the University of Cologne funded by the BMBF and uses resources from Intergenomics such as PRODORIC database Literature:
PMID: 17202169
SYSTOMONAS--an integrated database for systems biology analysis of Pseudomonas.
Choi C, Münch R, Leupold S, Klein J, Siegel I, Thielen B, Benkert B, Kucklick M, Schobert M, Barthelmes J, Ebeling C, Haddad I, Scheer M, Grote A, Hiller K, Bunk B, Schreiber K, Retter I, Schomburg D and Jahn D. (2007)
Nucleic Acids Res. 35 (Database issue), D553-D556
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TRANSCompel
 | database that contains composite elements of transcriptional regulation
Literature:
PMID: 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
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TRANSFAC
 | 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. Literature:
PMID: 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
PMID: 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
PMID: 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
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TRANSPATH
 | database on signal transduction networks in eukaryotes: The database focusses on data about mammalian organisms and provides links to gene regulation. Literature:
PMID: 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
PMID: 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
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VBase2
 | VBASE2 is an integrative database of immunoglobulin germ-line V gene
sequences, linking to the EMBL, Ensembl, IMGT, KABAT and VBASE database. Literature:
PMID: 15608286
VBASE2, an integrative V gene database.
Retter I, Althaus HH, Münch R and Müller W (2005)
Nucleic Acids Res. 33 (Database issue), D671-D674
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Virtual Footprint
 | bioinformatic tool that represents together with the PRODORIC database (containing transcriptional networks of prokaryotes) an integrative framework for regulon prediction in prokaryotes. It uses the weight-matrix approach and matrices from PRODORIC to identify target genes of bacterial and archaeal transcriptional regulators. Literature:
PMID: 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
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