Bioinformatics

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Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches.

List of subject category of interest, which may include Bioinformatics, Cancer, Genomics, Medical Genomics or one of the numerous other subject areas covered in this thematically- arranged index.

Comprehensive Enzyme Information System
BRENDA compiles comprehensive enzyme functional data from the primary literature and makes it available to the scientific community. It is available free of charge for researchers and non-profit organizations.

Broad Institute was launched in 2004 by MIT and Harvard to improve human health. Data produced and analytical software tools developed by The Broad Institute are openly shared with the entire scientific community. Data is arranged by organism/species, with links to relevant tools and project information; software tools allow for analysis of genome-related datasets.

Cn3D is a visualization tool for biomolecular structures, sequences, and sequence alignments which allows users to view 3-dimensional structures from NCBI's Entrez retrieval service. Cn3D offers annotation and alignment editing features. This free, downloadable application runs on Windows, Macintosh, and Unix platforms.

NCBI's retrieval system which integrates data from the major DNA and protein sequence databases along with taxonomy, genome, mapping, protein structure and domain information, and the biomedical journal literature via PubMed. Genome, Nucleotide, Protein and Structure are all available via the University Libraries Databases list.

(Expert Protein Analysis System) - Proteomics server of the Swiss Institute of Bioinformatics (SIB) dedicated to the analysis of protein sequences and structures as well as 2-D PAGE. It is expected to be renamed as SIB Bioinformatics Resource Portal in Spring 2011 and upgraded to include access to scientific databases and software tools in different areas of life sciences including proteomics, genomics, phylogeny, systems biology, population genetics, transcriptomics etc. This new portal is presently available as ExPASy-beta.

A database of Drosophila genes and genomes.

GenBank® is the NIH genetic sequence database, an annotated collection of all publicly available DNA sequences. Complete bimonthly releases and daily updates (incorporating international data) are available by FTP.

- Gene maintains information about genes from genomes of interest to the RefSeq group.

GOLD (Genomes Online Database) is an online resource for comprehensive access to information regarding complete and ongoing genome projects, as well as metagenomes and metadata, around the world.

at the Institute of Medical Genetics in Cardiff - HGMD represents an attempt to collate known (published) gene lesions responsible for human inherited disease. The public version of this database is freely available to users from academic institutions and non-profit organizations. Free registration is required.

Links to various software, mathematical tools, and databases to assemble and analyze genomic data.

NCBI provides access to biomedical and genomic information for use by researchers and the medical community via the creation of databases and tools for storing and analyzing knowledge about molecular biology, biochemistry, and genetics.

Online Bioinformatics Resources Collection - This collection from the University of Pittsburgh Health Sciences Library System provides several tools for finding information on genes and proteins, metabolic and signaling pathways, and experimental protocols.

The Pharmacogenomics Knowledge Base focuses on collecting, encoding, and disseminating knowledge about the impact of human genetic variations on drug response. They curate primary genotype and phenotype data, annotate gene variants and gene-drug-disease relationships via literature review, and summarize important PGx genes and drug pathways.

RCSB Protein Data Bank is an archive containing information about experimentally-determined structures of proteins, nucleic acids, and complex assemblies. Provides a variety of tools and resources allowing users to perform searches based on annotations relating to sequence, structure and function. All data is curated and annotated according to wwPDB standards.

(RefSeq) - RefSeq is a curated collection of DNA, RNA, and protein sequences. It provides one example of each natural biological molecule for major organisms ranging from viruses to bacteria to eukaryotes. For each model organism, RefSeq aims to provide separate and linked records for the genomic DNA, the gene transcripts, and the proteins arising from those transcripts.

Biology and genome of C. elegans

ZFIN - Zebrafish Information Network. Zebrafish model organism database of information for researchers.