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
