Literature search
|
| Entrez
PubMed |
PubMed, a service of the National Library of Medicine, provides
access to over 12 million MEDLINE citations back to the mid-1960's and
additional life science journals. PubMed includes links to many sites
providing full text articles and other related resources. |
| MeSH - Medical
Subject Headings |
It is designed to help quickly locate descriptors of possible
interest and to show the hierarchy in which descriptors of interest
appear. |
| OMIM -
Online Mendelian Inheritage in Man |
This database is a catalog of human genes and genetic
disorders. |
DNA sequence databases
|
| GenBank |
GenBank® is the NIH genetic sequence database, an annotated
collection of all publicly available DNA sequences. |
| EMBL über SRS@EBI |
The EMBL Nucleotide Sequence Database constitutes Europe's primary
nucleotide sequence resource. Main sources for DNA and RNA sequences
are direct submissions from individual researchers, genome sequencing
projects and patent applications. |
Protein sequence databases
|
| SWISS-PROT |
The Swiss-Prot Protein Sequence Database is a database of protein
sequences. It contains high-quality annotation,is non-redundant, and
cross-referenced to several other databases, notably the EMBL
nucleotide sequence database, PROSITE pattern database and PDB. |
| PIR |
The Protein Identification Resource consists of an integrated
computer system composed of a number of protein and nucleic acid
sequence databases and software designed for the identification and
analysis of protein sequences and their corresponding coding
sequences. |
Databases of Protein Motifs, Domains
|
| BLOCKS |
Blocks are multiply aligned ungapped segments corresponding to the
most highly conserved regions of proteins. Block Searcher, Get Blocks
and Block Maker are aids to detection and verification of protein
sequence homology. They compare a protein or DNA sequence to a database
of protein blocks (current version), retrieve blocks, and create new
blocks, respectively. |
| PROSITE |
PROSITE is a database of protein families and domains. It consists
of biologically significant sites, patterns and profiles that help to
reliably identify to which known protein family (if any) a new sequence
belongs |
| PRINTS |
PRINTS is a compendium of protein fingerprints. A fingerprint is a
group of conserved motifs used to characterise a protein family; its
diagnostic power is refined by iterative scanning of a
SWISS-PROT/TrEMBL composite. |
| PFAM |
Pfam is a large collection of multiple sequence alignments and
hidden Markov models covering many common protein families. |
| CATH |
CATH is a novel hierarchical classification of protein domain
structures, which clusters proteins at four major levels, Class(C),
Architecture(A), Topology(T) and Homologous superfamily (H). |
Protein Structure databases
|
| PDB - Protein
Database |
The Protein Data Bank (PDB) is an archive of experimentally
determined three-dimensional structures of biological macromolecules,
serving a global community of researchers, educators, and students. The
archives contain atomic coordinates, bibliographic citations, primary
and secondary structure information, as well as crystallographic
structure factors and NMR experimental data. |
Enzymes, reactions and metabolic pathway databases
|
| KEGG |
KEGG is a suite of databases and associated software, integrating
our current knowledge on molecular interaction networks in biological
processes (PATHWAY database), the information about the universe of
genes and proteins (GENES/SSDB/KO databases), and the information about
the universe of chemical compounds and reactions (COMPOUND/REACTION
databases). |
| ENZYME |
The ENZYME data bank contains the following data for each type of
characterized enzyme for which an EC number has been provided: EC
number, Recommended name, Alternative names, Catalytic activity,
Cofactors, Pointers to the Swiss-Prot entrie(s) that correspond to the
enzyme, Pointers to disease(s) associated with a deficiency of the
enzyme. |
| Roche Applied
Science "Biochemical Pathway" |
This page gives access to the digitized version of the Roche
Applied Science "Biochemical Pathways" wall chart. |
Gene ontology resources
|
| QuickGO |
The objective of GO is to provide controlled vocabularies for the
description of the molecular function, biological process and cellular
component of gene products. These terms are to be used as attributes of
gene products by collaborating databases, facilitating uniform queries
across them. The controlled vocabularies of terms are structured to
allow both attribution and querying to be at different levels of
granularity. |
Bioinformatics Tools
|
| FASTA |
Provides sequence similarity and homology searching against
nucleotide and protein databases using the Fasta programs. Fasta can be
very specific when identifying long regions of low similarity
especially for highly diverged sequences. You can also conduct sequence
similarity and homology searching against complete proteome or genome
databases using the Fasta programs. |
| BLAST |
BLAST® (Basic Local Alignment Search Tool) is a set of similarity
search programs designed to explore all of the available sequence
databases regardless of whether the query is protein or DNA. The BLAST
programs have been designed for speed, with a minimal sacrifice of
sensitivity to distant sequence relationships. |
| ClustalW |
Clustal W is a general purpose multiple sequence alignment program
for DNA or proteins.It produces biologically meaningful multiple
sequence alignments of divergent sequences. It calculates the best
match for the selected sequences, and lines them up so that the
identities, similarities and differences can be seen. |
