GENOMICS AND GENOME PROJECTS

See also our pages on BioInformatics and on the Trypanosoma cruzi Genome Initiative.

Already completed and still ongoing genome projects

"Genome projects never end"
Parasite Genome Projects
Bacteria
Yeast and other fungi
Invertebrate
Vertebrate
Human
Insects
Plants
Virusses
Organelles and endosymbiontes

Genome projects, listings and links at NCBI ; TIGR (complete genomes) and TIGR(incomplete genomes) ; Sanger ;
 

DATABASE SEARCHES AND RETRIEVAL (using keywords)

General Entrez searches, including genomes (using keywords, sequences etc.) and retrieval at NCBI-Genbank
Search dbEST, dbSTS, dbGSS general genome sequence databases.
Gene Indices (EST analyses) at TIGR.
CMR - Comprehensive Microbial Resourse (sequences and associated data) at TIGR

Sequence Retrieval System (SRS) at EBI , EMBL, Sanger,  Inst. Pasteur (Paris), at ExPASy (Switzerland)
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

NCBI ; EMBL  Blast Sequence Similarity Search (gapped blast and others)
Blast Searches at EMBnet-CH (includes TREMBL and others)
Search Parasite Genomes (EBI) and Parasite six frame translation searches (EBI)
Search Unfinished Microbial Genomes at NCBI or at TIGR
Fasta genome/proteome search and EST blast at EMBL
 

Comparative Genomics

COG's Clusters of orthologous groups at NCBI
TOGA Orthologous Gene Alignment (TIGR)
HOBACGEN Homologous Bacterial Genes
Sequences/Sources/Taxa database at TIGR

Sequencing and annotation

Sequencing protocols
ABI trace file analysis
Sequence annotation tools : ENSEMBL, ARTEMIS
Codon tables
Analyse your (hypothetical) gene and protein in-depth (Expasy and links)
Tools at the Institut Pasteur (Paris)
Alignments, frames, profiles etc. at EMBnet.CH

Bioinformatics for genome studies

Software tools

TIGR software tools
ACEDB software and info
Production software for sequencing and processing (Sanger)
 

BioInformatics/Computational Biology for Genomics

Sanger - Computational Genomics Group
EMBL - Biocomputing Unit
EMB-Net Centers
South African National Bioinformatics Institute
Univ. Pennsylvania Computational Biology and Informatics Lab.

Functional Genomics

Functional classification of genes, proteins and enzymes

Kinetoplastid gene/protein nomenclature and functional classification scheme
Yeast protein classification
Enzyme databases and nomenclature
Kegg metabolic pathways and searches
Boehringer Mannheim's Biochemical pathways
E. coli genes and biochemical pathways
WIT metabolic reconstructions
Yeast biochemical pathways
The Minimal Genome (TIGR)

MicroArray techniques

Microarray activities, resources and links at EBI, at TIGR,
 

Proteomics, Metabolomics

Proteomics tools (2D, mass-spec analyses, prot structure and function; at Expasy)
Parasite Proteome Analysis (EBI) and search facility
 

Methods, protocols, discussion groups and Newsletters

Molecular biology protocols (NWFSC)
Molecular biology protocols (MBS) (Molecular Biology Shortcuts)

Genome studies in Latin-America

Special links and additional information

Links to major Genome Centers
The Genome Sequence Database Homepage
A summary page of genome sequencing projects

FTP of Genome Databases and Software

Sanger Center
NCBI
TIGR