Bioinformatics Web Resources
Databases
DBCAT - the CATalog of DataBases
EMBL - European Molecular Biology Laboratory
Ensembl Genome Browser - produces and maintains automatic annotation on metazoan genomes
GDB - official world-wide database for the annotation of the human genome
GenBank - NCBI database and data mining tools
KEGG - database on molecular interaction networks, including metabolic pathways, regulatory pathways, and molecular complexes
NCBI - National Center for Biotechnology Information
PDB - repository for the processing and distribution of 3-D biological macromolecular structure data
Swiss-Prot - curated protein sequence database
TRANSCompel is a database on composite regulatory elements affecting gene transcription in eukaryotes
TRANSFAC is a database on eukaryotic transcription factors, their genomic binding sites and DNA-binding profiles. TRANSFAC is available at the Joslin Bioinformatics Core. Please contact Igor Leykin
TRANSPATH database provides information about signal transduction pathways, in particular those that aim at transcription regulatory components
TrEMBL - computer-annotated supplement of Swiss-Prot that contains all the translations of EMBL nucleotide sequence entries not yet integrated in Swiss-Prot
Software
Data Analysis and Integration
Bioconductor is an open source and open development software project for the analysis and comprehension of genomic data
ChipInfo - extracting gene annotation and Gene Ontology information for microarray analysis
GeneAnnot is Affymetrix microarray gene annotation
GeneCards is a database of human genes, their products and their involvement in diseases
GeneCruiser is a gene annotation tool
GeneLoc presents an integrated map for each human chromosome
GenMAPP - Gene Map Annotator and Pathway Profiler
GeneNote is a database of human genes and their expression profiles in healthy tissues
GeneNotes integrates various information about specific genes
GeneTide is an automated system for human transcripts (mRNA & ESTs)
annotation and elucidation of de-novo genes
GoSurfer - graphical data mining tool for microarray data using Gene Ontology information
The R Project for Statistical Computing
RESOURCERER provides annotation based on the TIGR Gene Indices (TGI) for commonly available microarray resources, including widely used clone sets and Affymetrix GeneChip Arrays
Microarray Data Analysis
Affymetrix Microarray Suite Software
Broad Institute Cancer Program Software (GenePattern, GeneCluster)
cDNA Microarray Analysis - quality filtering, channel normalization, models of variations and assessment of gene effects
ChipInfo - extracting gene annotation and Gene Ontology information for microarray analysis
Cluster- perform a variety of types of cluster analysis and other types of processing on large microarray datasets
DNA-Chip Analyzer (dChip) is a software package implementing model-based expression analysis of oligonucleotide gene expression and SNP arrays
GenePix Pro is a complete standalone image analysis software for microarrays, tissue arrays and cell arrays
GeneSpring is a software for gene expression analysis
Gifi Array Analyzer - analyzing microarray data with Homogeneity Analysis
GMEP (available for Unix only) - compute genome-mean expression profiles from expression and sequence data
Maple Tree is a java-based, open source, cross-platform visualization tool to graphically browse the results of clustering analyses from the Cluster software
Rosetta Resolver is a global gene expression research system providing quality data analysis
R-SVM - recursive sample classification and gene selection with SVM for microarray data
ScanAlyze - process fluorescent images of microarrays
TightClust - resampling based clustering method for microarray data
TreeView - graphically browse results of clustering and other analyses from Cluster software
Sequence Analysis
BioOptimizer - bayesian scoring method for comparing and optimizing regulatory motif predictions from AlignACE, BioProspector, CONSENSUS, and MEME
BioProspector - web-interactive algorithm for finding gene regulatory binding motifs
CisModule - de novo discovery of cis-regulatory modules
CompareProspector - eukaryotic regulatory element conservation analysis and identification using comparative genomics
GATA - Graphic Alignment Tool for comparative sequence Analysis
Gibbs Motif Sampler - UNIX (Sun OS) software to search for multiple motifs with unknown number of repeats in multiple protein sequences
GMEP (available for Unix only) - compute genome-mean expression profiles from expression and sequence data
MDScan - algorithm for finding protein-DNA interacting sites (gene regulatory binding motifs) from the 5' untranslated sequences selected by Chromatin-immunoprecipitation microarray (ChIP-array) and other microarray experiments
Motif Regressor - algorithm for integrating sequence motif discovery with measures from mRNA expression microarray or Chromatin-Immunoprecipitation microarray (ChIP-chip) experiments
TFEM - Transcription Factor Expectation Maximization, an algorithm for detecting DNA regulatory motifs by incorporating positional trends in information content
SNP and Linkage disequilibrium Analysis
BLADE - Bayesian LinkAge DisEquilibrium mapping algorithm based on Liu et al. (2001) published in Genome Research
DNA-Chip Analyzer (dChip) is a software package implementing model-based expression analysis of oligonucleotide gene expression and SNP arrays
HAPLOTYPER Users’ Documentation for SNP haplotype reconstruction based on the Partition-Ligation method (Niu et al. 2002) published in Am. J. Hum. Genet.
The International HapMap Project is a multi-country effort to identify and catalog genetic similarities and differences in human beings
PHASE - software for haplotype reconstruction, and recombination rate estimation from population data
Please send your suggestions to Igor Leykin