BIOINFORMATICS
The purpose of this page is to provide you with links for WWW based on-line
nucleotide and protein sequence analysis, for database access, general
information regarding bioinformatics including tutorials, and information
about ftp sites for software download.
For Genomes and Genomics, see our GENOMICS
pages.
Sites who provide www based services permit data entry by database
accession number or "cut-paste" of your own sequence, usually in plain,
continuous format without extra symbols (e;g; "fasta" format). So have
your sequence ready in your Windows clipboard for pasting!
DATABASE SEARCHES AND RETRIEVAL (using keywords)
General Entrez searches
(Sequences, Genomes, PubMed, Population data, PDB) and retrieval at NCBI-Genbank
Search dbEST, dbSTS,
dbGSS
general genome sequence databases.
Sequence Retrieval System (SRS) at EBI
, EMBL, Sanger,
Inst. Pasteur (Paris), at ExPASy
or choose
from LIST
DBGET/LinkDB Integrated
database retrieval system (Japan)
Search Swissprot/TREMBL -
PROSITE
(protein and patterns dictionary) databases
ProDOM and
DOMO
protein domain databases
Pfam Protein Families database at Sanger
(UK) or UW (USA)
Enzyme and metabolic
databases
Vector Database
Sequence databases at Inst.
Pasteur (Paris)
BLAST SEARCHES WITH NUCLEOTIDE AND PEPTIDE SEQUENCES
BLAST Sequence Similarity
Search (gapped blast and others) at NCBI.
Blast
Searches at EMBnet-CH (includes TREMBL and others)
Search Parasite
Genomes (EBI)
Search unfinished
microbial genomes (NCBI)
GENERAL SEQUENCE ANALYSIS TOOLS AND SUPPORT
BioComputational Services and
Tools
at EMBL
Analyse your (hypothetical) gene
and protein in-depth (Expasy and links)
Tools at the Institut Pasteur
(Paris)
Alignments, frames, profiles etc. at EMBnet.CH
DEPOSIT OF SEQUENCES TO DATABASES
To Genbank
To dbEST
To dbSTS
To dbGSS
To EMBL
GENE FINDING AND CHARACTERIZATION
Find ORFs (NCBI)
Translate your nt
sequence in hypothetical protein
Try different gene
and exon predictions
PROTEIN STRUCTURE AND FUNCTION ANALYSIS
Expasy Protein databases (Swissprot;
TREMBL), 2D and 3D data, PROSITE, enzyme nomenclature etc.
Expasy Protein characterization,
structure analysis, similarity, pattern and profile searches etc.
NCBI Entrez
3D structure database and Protein
Structure database.
BIOCHEMICAL PATHWAYS
Kegg metabolic pathways
and searches
Boehringer Mannheim's Biochemical
pathways
E. coli genes and biochemical
pathways
WIT metabolic reconstructions
Yeast
biochemical pathways
SPECIAL SITES
Codon Tables
PHYLOGENY SOFTWARE AND INFORMATION
The Tree of Life
Taxonomy
at NCBI
Ribosomal Database Project
Treebase, a database
of trees and phylogeny sources (Harvard)
Species2000, the world species
index
IF YOU DID NOT FIND A SUITABLE LINK ON OUR SITE ...
The BioNetbook Web page
directory for Biology
Amos' WWW links page
Pedro's
BioMolecular Research Tools
BioHunt Molecular Biology
Finder
Expasy
EMBnet links to all individual
member centers
DBCat,
a catalog of databases
A Mol
Biol Database list
General BioInformatics
Biopages at Harvard
BIOINFORMATICS AND COMPUTATIONAL BIOLOGY IN LATIN-AMERICA
Soon here : directory of research groups and people
TUTORIALS ON BIOINFORMATICS
BIOSCI/Bionet communications forum
BioInformatics
guide for sequence analysis (Martin Aslett)
AAnP - IUPAC-IUBMB
nomenclature for amino acids and peptides
Carbohydrates
- IUPAC-IUBMB nomenclature for carbohydrates
Genetic
codes - List of non-standard genetic codes from NCBI
Sequence similarity
searches primer (Keith Robison, Harvard)
Pedestrian
guide to analysing sequence databases (Rost and Schneider, EMBL)
Biocomputing
courses resource list - Syllabi and tutorials on Bioinformatics (VSNS
BCD)
Biocomputing
tutorials - EMBnet Biocomputing tutorials
BioComputing
Hypertext Coursebook - (VSNS BCD)
BioActivity
- Protein sequence and structure analysis: a practical guide
Homology modeling
course (EMBL)
BioInformatique,
par SIS (Inst. Pasteur, Paris)
FTP SITES FOR SOFTWARE AND DATABASES
Genbank database
EMBL database
Swissprot
database
SANGER Center
NCBI : Sequence comparison
software, contributed programs, Genbank, toolbox etc.
EMBOSS software
suite (EMBL/Sanger)
A Bio-software index
Bio-Access guide
Software for Unix, PC, Mac at Inst.
Pasteur (Paris) or search the BioCatalog