ARTS - ARTS (Advanced Retrieval Tool for SNPs) can be used to retrieve
SNP that are polymorphic between several different mouse strains to aid in the
design of genome-wide SNP marker panels.
BLAST - Basic Local Alignment Search Tool;
retrieve sequences similar to your query.
BankIt - Web-based submission of one or a few sequences to GenBank.
Cancer Genome Anatomy Project - Goal is to determine the gene expression profiles of normal,
precancer, and cancer cells; resources for human and mouse include ESTs, gene
expression patterns, SNPs, cluster assemblies, cytogenetic information, and tools
to query and analyze the data.
dbSNP - Repository for both single base
nucleotide subsitutions and short deletion and insertion polymorphisms; NCBI
collaboration with NHGRI.
EBI Tools - EBI Tools is a project that aims to provide programmatic
access to the various databases and retrieval and analysis services EBI
provides through Simple Object Access Protocol (SOAP) and other related web
Electronic PCR - Find sequence-based markers (STSs) and therefore, map
location in a DNA sequence of interest; useful for detecting mis-priming events.
EMBOSS - Diverse suite of tools for sequence analysis; many programs
analagous to GCG; context-sensitive help for each tool.
Entrez - NCBI information retrieval system, including GenBank, MMDB
(structures), genomes, population sets, OMIM, taxonomy and PubMed.
FeatureExtract - The FeatureExtract server extracts sequence and feature
annotations, such as intron/exon structure, from GenBank entries and other GenBank
Genelynx - A portal to the human genome. Query by text or BLAST,
to access heaps of info from primary and secondary databases of genomic resources,
transcripts, protein sequences, function, associated diseases, homologs, ests.
GtRDB - GtRDB: The Genomic tRNA Database Automated tRNA identifications
by the program tRNAscan-SE on complete or nearly complete genomes.
MicroInspector - MicroInspector is a tool that detects miRNA (microRNA)
binding sites in your input sequence by searching against databases of known miRNA
miRU - miRU is a tool that takes as an input a small miRNA sequence and
then searches for complementary matches in TIGR plant-specific gene data sets to
predict potential target genes.
Non-Coding RNA database - Non-translatable RNA transcripts that appear to
work at the RNA level.
International HapMap Project - The haplotype map, or HapMap, is a tool that will allow
researchers to find genes and genetic variations that affect health and disease.
Oligodb - Oligodb generates oligos suitable for expression experiments
based on predicted gene transcripts from the Ensembl project. One can search for
transcripts via keyword, or do a batch search by providing a list of Ensembl identifiers.
OligoWiz - OligoWiz 2.0 is a client for microarray probe design that
allows for the integration of sequence annotations, probe quality parameters, and
the placement of multiple probes per transcript.
Sequin - Desktop tool developed by the NCBI for editing, annotating and
submitting DNA sequences to any of the three DNA sequence submission sites (DDBJ,
EMBL or GenBank).
MartView - The Ensembl EnsMart Genome Browser (MartView) is a tool for
data retrieval and data mining that integrates data from Ensembl. Through the web
interface MartView allows you to apply a series of filters to create custom datasets
which can be converted to several useful output formats.
MRS - MRS is a biological data retrieval system that can be accessed
over the web, or installed and used locally. MRS indexes several flat-file data sets
for searching, including EMBL nucleotide, UniProt, PDB and KEGG. Searches can be
performed globally, or on one or more flat file fields per data set.
Primer3 - Comprehensive PCR primer and hybridization probe design tool; many
options but easy to accept defaults at first.
Riboswitch finder - RNA motif search program that identifies RNA motifs called
riboswitches which are metabolic binding domains in mRNA that regulate gene
expression. The program was originally designed around a set of riboswitches found
in Bacillus subtilis.
RNAbase - RNAbase is a searchable and annotated database of all publicly
available RNA structures.
SOURCE - Stanford Online Universal Resource for Clones and ESTs pools
publicly available data commonly sought for any clone, GenBank accession, or gene
from human, mouse, rat.
SRS - Sequence Retrieval System network browser for multiple molecular
WEBIN - WEBIN is the internet tool for the submission of nucleotide
sequences to the EMBL database. It is a service offered by the European
Bioinformatics Institute (EBI), an outstation of the European Molecular Biology
WU BLAST - Washington University Basic Local Alignment Search Tool.
3D-pssm - Protein fold recognition using 1d and 3d sequence profiles
coupled with secondary structure and solvation potential information.
AISMIG - AISMIG (An Interactive Server-side Molecule Image Generator) is
a tool for generating and visualizing high resolution 3D images from PDB structure
AS2TS - The AS2TS (Amino acid Sequence to Tertiary Structure) system
consists of servers for protein structure analysis and modelling.
BhairPred - BhairPred is a tool for predicting beta-hairpins in protein
sequences using a support vector machine.
BioInfo3D - BioInfo3D is a collection of tools for the structural
analysis of proteins, including tools for structural alignments and prediction
of protein interactions.
Bioverse - Bioverse is a system that uses computational techniques to
facilitate exploring the relationships between molecular, genomic, proteomic,
systems and organismal information.
BSDD - BSDD (Biomolecules Segment Display Device) searches for and
displays user defined sequence motifs in known protein structures. This web based
tool incorporates the graphics package of RASMOL for visualization.
CD-Search - CD-Search allows the user to search the Conserved Domain Database
(CDD) for conserved structural and functional domains in a sequence of interest;
links to 3-D structures where applicable.
Cn3D - Web browser helper application that simultaneously displays
3-D structure, sequence, and alignment.
ConSeq - ConSeq is a tool for predicting functionally and structurally
important amino acid residues in protein sequences. The predictions are based on
the assumptions that residues of functional importance are often conserved and
solvent-accessible, and those of structural importance are often conserved and
located in the protein core. A multiple sequence alignment is used to predict
the relative solvent accessibility state and the evolutionary rate at each residue.
ElNemo - ElNemo (The Elastic Network Model) is a tool for predicting the
possible movements (ie. conformational changes and other structural changes) of
macromolecules. This tool allows users to compute, visualize, and analyse
low-frequency normal modes of a protein.
DeNovoID - DeNovoID is a tool for protein identification using de novo
peptide sequence data from mass spectrometry experiments.
ExPASy Proteomics tools - Various tools for protein identification and
characterization, similarity searches, pattern and profile searches,
post-translational modification prediction, and more.
GELBANK - GELBANK is a database of 2D gel images of proteomes for species
with completed genomes. The user can search by sequence description or fragment, or
by gel characteristics. Links are made between the sequence and gel when available.
GoMiner - GoMiner organizes and allows the visualization of large sets of
genes based on Gene Ontology classifications.
Human Protein Reference Database - The Human Protein Reference Database
(HPRD) is a centralized resource for information about human proteins, their
interactions with other human proteins, and protein-disease relationships. The
information contained in HPRD is curated by experts, who manually extract it from
MINER - MINER is a tool for the identification and visualization of
phylogenetic motifs (regions within a multiple sequence alignment (MSA) that
conserve the overall phylogeny of the complete family).
MMDB - Molecular Modelling Database of 3-D structures; experimentally
determined structures only.
MolMovDB - The Database of Macromolecular Movements (MolMovDB) contains a
collection of animated protein and RNA structures to assist in the exploration of
macromolecular flexibility. Software for structure analysis is also available.
MONSTER - MONSTER takes a PDB structure file as input, and predicts
non-bonding interactions that have the potential to provide stability to the molecule. The output can be viewed or downloaded as XML or text, or can be viewed as a 3D structure or a 2D diagram. There is also a good tutorial available at the site.
PDB - Protein Data Bank; includes theoretical structures.
PDB2PQR Server - Server that allows users to convert PDB files into PQR
files by adding missing atoms, optimizing hydrogen bonding and assigning atomic
charge and radius parameters. The resulting PQR file can be used for electrostatic
calculations which can give insight into the influence of electrostatics on
ProteinDBS - ProteinDBS takes a PDB ID or structure as input, and searches for
similar protein tertiary structures using computer visualization techniques. The
superposition of structures and the aligned component of the sequence can then be
viewed over the web.
RasMol - 3-D structure viewer, web browser helper application.
SPACE - SPACE (Structure Prediction and Analysis based on Complementarity
with Environment) is a suite of tools for predicting and analyzing structures of
biomolecules and their complexes.
STRAP - The Structural Alignment Program for Proteins (STRAP) is a
java-based program that can be run over the web using a Java Web Start enabled
browser or downloaded and run as a stand-alone application. Alignments can be done
using one of several methods, including ClustalW, JAligner and T_coffee. STRAP is
also able to incorporate structure information and interfaces with programs such as
Pymol and Rasmol. There is also a tutorial included.
Swiss-Prot and TrEMBL - Swiss-Prot is a curated database of protein sequences that are
highly annotated and have a minimal level of redundancy. TrEMBL is a supplement to
Swiss-Prot, containing computer-annotated translations of EMBL sequences.