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National Center for Biotechnology Information http://www.ncbi.nlm.nih.gov/ Genetics Computing Group
(GCG package)
Human Genome Browser at UC
Santa Cruz
Mouse Genome Informatics
(Jackson Laboratories)
TIGR - The Institute for
Genomic Resources
UK Human Genome Mapping Project
Resource Centre
European Bioinformatics Institute
(EMBL) - Database Searching, Browsing and Analysis Tools
CINEMA - Color INteractive
Editor for Multiple Alignments
KEGG (Kyoto University Encyclopedia
of Genes and Genomes) database of metabolic pathway and regulatory pathway
genes, etc.
MathInspector from GenoMatrix
(public domain)
Caltech Genome Research Laboratory
- Links to WWW sites for genome informatics, nomenclature, development,
anatomy, cell and animal physiology, laboratory animal suppliers, veterinary
resources and animal husbandry, regulations and legal issues, software,
technical guides and protocols, printed text and videos, conferences, etc.
Weizmann Institute Bioinformatics
AceView feature from NCBI
EPD: Eukaryotic Promoter
Database (Epalinges/Lausanne)
Ensembl is a joint project
between EMBL-EBI and the Sanger Centre to develop a software system which
produces and maintains automatic annotation on eukaryotic genomes. Human
and mouse data are available now; worm will be added soon.
Prostate Expression Database
The Sanger Centre is a genome
research centre founded by the Wellcome Trust and the Medical Research
Council. Our purpose is to further the knowledge of genomes, particularly
through large-scale sequencing and analysis.
MIRAGE server
Biocomputing Service Group
(DKFZ, Heidelberg)
GeneCards™ is a database
of human genes, their products and their involvement in diseases. It offers
concise information about the functions of all human genes that have an
approved symbol, as well as selected others.
The EMBOSS Applications
Transcription Factor Search
- TFSearch
Transcription Element Search
System (TESS) is a set of software for locating and displaying transcription
factor binding sites in DNA sequence. TESS uses the Transfac database as
its store of transcription factors and their binding sites.
WebGene – Tools For Prediction
And Analysis Of Protein-Coding Gene Structure: An integrated computing
system for protein-coding gene prediction, Gene structure prediction using
information on homologous protein sequence, EST Mapping, CDS prediction
based on Silent/Replacement ratio, Repeated elements mapping, CpG islands
prediction, Splicing signals prediction, Hamming Clustering Method for
Poly-A prediction in Eukaryotic Genes, Hamming Clustering Method for TATA
signal prediction in Eukaryotic Genes, A computing system for protein-coding
gene prediction.
CpGPlot will produce a parameter
report along with a graph depicting the Obs/Exp, %CG and Putative Islands
plots. CpGReport will produce an EMBL formated report with a Feature Table
that contains a Key for each island found along with location/qualifiers
that depict the position of the island, its size, the total sum of C+G's
in the island, the %CG and the observed/expected value max for it. At the
bottom of each report the total number of islands found is printed or a
'No islands found' text.
NEBcutter V1.0
CLUSTALW software
BOXSHADE 3.21 (software with
which to format alignments for further publication).
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