Bioinformatics 

Items listed in the Databases and Tools box is not a complete list, just a selection of commonly used resources. If you have a suggestion, please add it here!

  

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Proteins

BIOBASE (MIT only) --  integrated analysis tools coupled with computational and experimental data for drug discovery, biomarker discovery, gene regulation analysis and more.

• Proteome - a comprehensive resource for the proteins of YPD, HumanPSD, WormPD, GPCR-PD, PombePD, and MycopathP.
• TransFac - contains data on transcription factors, their experimentally-proven binding sites, and regulated genes.
• TransPath - provides information on signaling molecules, metabolic enzymes, second messengers, endogenous metabolites, miRNAs and the reactions they are involved in.
• ExPlain - biological analysis tool for large-scale data, such as gene expression, proteomics and ChIP-chip data.

Protein Data Bank --  tools and resources for studying the structures of biological macromolecules and their relationships to sequence, function, and disease

Expert Protein Analysis System (ExPASy) -- portal containing tools and databases for molecular biology analysis.

NCBI

• MMDB: Structure  -- a database of experimentally determined three-dimensional biomolecular structures
• Protein -- a database of protiens compiled from a variety of sources, including SwissProt, PIR, PRF, PDB, and translations from annotated coding regions in GenBank and RefSeq
• BLASTp- alignment tool that finds regions of similarity between protien sequences.

Uniprot -- a central repository of protein sequence and function created by joining the information contained in Swiss-Prot, TrEMBL, and PIR

Ensembl - software system which produces and maintains automatic annotation on selected eukaryotic genomes.

GenePattern -- analysis workflow tool developed to support multidisciplinary genomic research program.

Nucleic Acids

NCBI

• GenBank -- the NIH genetic sequence database, an annotated collection of all publicly available DNA sequences.
• Nucleotide -- a collection of sequences from several sources, including GenBank, RefSeq, and PDB.
• BLASTn -- finds regions of similarity between nucleotide sequences.

GenePattern -- analysis workflow tool developed to support multidisciplinary genomic research program.

Ensembl - software system which produces and maintains automatic annotation on selected eukaryotic genomes.

EMBL Nucleotide Sequence Database -- Europe's primary nucleotide sequence resource.

Genes and Genomes

Biobase's ExPlain [MIT only] -- biological analysis tool for large-scale data, such as gene expression, proteomics and ChIP-chip data.

Ensembl - software system which produces and maintains automatic annotation on selected eukaryotic genomes.

GenePattern -- analysis workflow tool developed to support multidisciplinary genomic research program.

NCBI

• Gene -- searchable database of genes, from RefSeq genomes, and defined by sequence and/or located in the NCBI Map Viewer
• Genome - provides views for a variety of genomes, complete chromosomes, sequence maps with contigs, and integrated genetic and physical maps. The database is organized in six major organism groups: Archaea, Bacteria, Eukaryotae, Viruses, Viroids, and Plasmids and includes complete chromosomes, organelles and plasmids as well as draft genome assemblies.
• Genome Project - The human genome project is the result of an international consortium among many different sequencing and bioinformatics centers. A wealth of data is available including; the annotated assembled genomic sequence, transcript sequence, library resources, expression data, map data, disease and functional information, and more.
• Map Viewer - supports search and display of genomic information by chromosomal position.

UCSD Genome Browser - Bioinformatics and Systems Biology, University of California at San Diego.  Projects include genome annotation, protein sequence-structure mapping, functional genomics, reconstruction and modeling of biochemical pathways, infrastructure for biological databases – analysis tools & interfaces.

Ensembl - software system which produces and maintains automatic annotation on selected eukaryotic genomes.

Organisms and Phylogeny

NCBI

• Taxonomy -- contains the names of all organisms that are represented in the genetic databases with at least one nucleotide or protein sequence

MGI: Mouse Genome and Informatics -- international database resource for the laboratory mouse, providing integrated genetic, genomic, and biological data to facilitate the study of human health and disease.

SGD: Saccharomyces Genome Database -- contains the molecular biology and genetics of the yeast Saccharomyces cerevisiae, which is commonly known as baker's or budding yeast

Flybase -- contains the Drosophila Genes and Genomes

NIH Rat Genomics and Genetics -- serves as a central point for information on National Institutes of Health (NIH) sponsored and related rat genetic and genomic activities and resources

WormBase -- is an international consortium of biologists and computer scientists dedicated to providing the research community with accurate, current, accessible information concerning the genetics, genomics and biology of C. elegans and some related nematodes

ZFIN: The Zebra Fish Model Organism Database -- is a zebrafish model organism database for genetic, genomic and developmental information

Expression

NCBI

• GENSAT -- is the gene expression nervous system atlas that aims to map the expression of genes in the central nervous system of the mouse, using both in situ hybridization and transgenic mouse techniques
• PROBE -- is a public registry of nucleic acid reagents designed for use in a wide variety of biomedical research applications, together with information on reagent distributors, probe effectiveness, and computed sequence similarities
• GEO: Gene Expression Omnibus -- is a gene expression/molecular abundance repository supporting MIAME compliant data submissions, and a curated, online resource for gene expression data browsing, query and retrieval

Biobase's ExPlain [MIT only] -- biological analysis tool for large-scale data, such as gene expression, proteomics and ChIP-chip data.