Online Databases
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BLAST
The 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.
BLAST can be used to infer functional and
evolutionary relationships between sequences as well
as help identify members of gene families.
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Circadian Gene Expression Database
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DAVID
The Database for Annotation,
Visualization and Integrated Discovery
(DAVID) 2006 is an expanded version of
original web-accessible program. DAVID
provides a comprehensive set of functional
annotation tools for investigators to
understand biological meaning behind large
list of genes.
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Ensemble Genome Browser
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Entrez
Entrez is a powerful federated search
engine, or web portal that allows users to
search a multiple of discrete health
sciences databases, maintained by the
National Center for Biotechnology
Information with a single query string and
user interface.
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NCBI Genbank
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NCBI Pubmed
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PDB
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UCSC Genome Browser
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UniProtKB/Swiss-Prot
The UniProtKB/Swiss-Prot Protein
Knowledgebase is a curated protein sequence
database that provides a high level of
annotation, a minimal level of redundancy
and a high level of integration with other
databases. Together with UniProtKB/TrEMBL,
it constitutes the UniProt Knowledgebase,
one component of the Universal Protein
Resource (UniProt), a one-stop shop allowing
easy access to all publicly available
information about protein sequences.
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Symatlas
SymAtlas is a web-application for
publishing experimental gene
functionalization datasets integrated with a
flexibly searchable gene-centric database of
public and proprietary annotations.
Bioinformatics Software
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HMMER
HMMER is an implementation of profile
hidden Markov model (HMM) methods for
sensitive database searches using multiple
sequence alignments as queries.
HMMER takes a multiple sequence
alignment as input. It can then build a
statistical model called a "hidden Markov
model" which can be used as a query into a
sequence database to find (and/or align)
additional homologues of the sequence
family.
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R
R is a language and environment for
statistical computing and graphics,
itprovides a wide variety of statistical
(linear and nonlinear modelling, classical
statistical tests, time-series analysis,
classification, clustering, ...) and
graphical techniques, and is highly
extensible.
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Bioconductor
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BLAT
A tool performs rapid mRNA/DNA and
cross-species protein alignments.
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Cluster and Treeview
Cluster and TreeView are an integrated
pair of programs for analyzing and
visualizing the results of complex
microarray experiments.
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Genscan
GENSCAN is a program designed to predict
complete gene structures, including exons,
introns, promoter and poly-adenylation
signals, in genomic sequences. It differs
from the majority of existing gene finding
algorithms in that it allows for partial
genes as well as complete genes and for the
occurrence of multiple genes in a single
sequence, on either or both DNA strands.
Program versions suitable for vertebrate,
nematode (experimental), maize and
Arabidopsis sequences are currently
available. The vertebrate version also works
fairly well for Drosophila sequences.
Sequences can be submitted on a web-based
form at this site.
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Ruby
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BioRuby
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Perl
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BioPerl