SEQUENCE DATABASES & RETRIEVAL SYSTEMS

The major sequence retrieval systems
These systems use the sequence databases listed in Major public sequence databases below.

NCBI Entrez (USA), also contain PubMed literature DB (Medline).
   http://www.ncbi.nlm.nih.gov/Entrez/ NEW: Search all DB
   http://www.ncbi.nlm.nih.gov/entrez/ OLD: Choose DB
SRS (Europe, several sites)
   http://srs.ebi.ac.uk
   http://srs.sanger.ac.uk
   Lund http://titanic.thep.lu.se

Major public sequence databases
These databases belongs to the International Nucleotide Sequence Database Collaboration and they exchange data daily. As each member database stores and presents the underlying data using a slightly different format, this data exchange makes all known nucleotide and protein sequence data available to all users, regardless of which of the three databases are queried.

Expressed sequence tag clustering databases
The ability to bring together expressed sequence tag, mRNA and other related sequences into gene-oriented clusters often facilitates genomic analysis, since the method groups individual sequences that most likely arise from the same gene or transcript. These three databases provide gene-oriented views of the data, using different algorithms in calculating the individual gene clusters.

STRUCTURAL/SECONDARY DATABASES

Alternative splicing databases
EBI: Alternative Splicing Database (ASD = AltSplice, AltExtron, AEdb)
   http://www.ebi.ac.uk/asd/
UCLA: Alternative splicing annotation project (ASAP = HASDB)
   http://www.bioinformatics.ucla.edu/ASAP/

Protein/RNA secondary databases
Human Protein Reference db
   http://www.hprd.org/
PROSITE (patterns, profiles)
   http://www.expasy.org/prosite/
Protein families database (Pfam)
   http://www.sanger.ac.uk/Software/Pfam/
NCBI Conserved Domain Database (= Pfam+SMART)
   http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml
EBI InterPro (=Pfam,PROSITE,SCOP, ...))
   http://www.ebi.ac.uk/interpro/
Rfam (RNA covariance models)
   http://www.sanger.ac.uk/Software/Rfam/

Structural databases
These databases have information on the 3D structure of sequences.

Protein Data Bank (PDB)
   http://www.rcsb.org/pdb/
Nucleic Acid Database (NDB)
   http://ndbserver.rutgers.edu/
NCBI mmdb (subset PDB)
   http://www.ncbi.nlm.nih.gov/Structure/MMDB/mmdb.shtml

OTHER DATABASES

GENOME INFORMATION

Genome Browsers

Ensembl
   http://www.ensembl.org
NCBI Map Viewer
   http://www.ncbi.nlm.nih.gov/cgi-bin/Entrez/map_search
UCSC Genome Browser
   http://genome.ucsc.edu
Celera
   http://www.celera.com/genomics/academic/home.cfm
ORNL Genome Channel
   http://compbio.ornl.gov/channel/
RIKEN Genomic Sciences Center
   http://hgrep.ims.u-tokyo.ac.jp/
VISTA (homology)
   http://pipeline.lbl.gov/cgi-bin/gateway2

Genome annotation
The following sites provide detailed information on annotations at each of the three major genome portals.

Human Genome Hub and Genome Central
These sites provide jumping-off points to major genome-based web sites. Resources available include trace data archives, access to cDNA and expressed sequence tag data and mapping information used to produce genome assemblies. The web sites of the individual members of the International Human Genome Sequencing Consortium may be accessed through these sites.

Human genetic and physical maps
The databases listed below represent a significant portion of the data underlying current human genome assemblies. Many of these data are available through DDBJ/EMBL/GenBank, but each database contains additional information regarding clones, constructs and similar that is not available through the major sequence repositories. A more extensive list of human genetic and physical maps can also be found through the online Nucleic Acids Research Database Collection, at http://nar.oupjournals.org/cgi/content/full/30/1/1/DC1.

Genomic Databases and Resources
Useful databases containing human mutation, variation, medical or expression data. The list is a short representative cross-section of the types of database freely available to genome researchers. See also the 'lists of lists' found at the Human GenomeHub and Genome Central cites for a more extensive list.

EDUCATION & ETHICS

Genetic education
The following sites present basic information on genetics and genomics, much of which is appropriate for elementary and secondary school education, as well as for the college level. Many of these sites offer teaching plans, graphics and other teaching resources that can be freely used in the classroom or lecture hall.

Ethical, legal and social Issues
Ethical, legal and social issues (ELSI) are becoming increasingly important in this age of genetic and genomic research. The following web sites provide an introduction to important issues related to genome biology as applied to human health and provide a jumping-off point for further information.

SEARCHING FOR MATCHES IN DATABASES

Sequence-based searching
List of sequence similarity search tools can be found on the ExPASy web site, at http://us.expasy.org/tools/.

BLAST
   http://www.ncbi.nlm.nih.gov/BLAST/
Mega-BLAST with Trace DB (Cross-species)
   http://www.ncbi.nlm.nih.gov/blast/tracemb.shtml
BLAT
   http://genome.ucsc.edu/cgi-bin/hgBlat?command=start
Ensembl BLAST
   http://www.ensembl.org/Homo_sapiens/blastview
SSAHA
   http://trace.ensembl.org/perl/ssahaview
EnsMART
   http://www.ensembl.org/Multi/martview?

Pattern/domain/profile-based searching
PROSITE
   http://us.expasy.org/tools/scanprosite/
MotifScan (Prosite patterns/profiles + Pfam)
   http://hits.isb-sib.ch/cgi-bin/PFSCAN?
NCBI Conserved Domain Database (= Pfam+SMART)
   http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=cdd
InterPro scan
   http://www.ebi.ac.uk/InterProScan/
Pfam (protein HMM models)
   http://www.sanger.ac.uk/Software/Pfam/
   http://pfam.cgb.ki.se/
Rfam (RNA covariance models)
   http://www.sanger.ac.uk/Software/Rfam/

Structure-based searching/prediction
TMHMM, SignalP, TargetP, ChloroP (and more)
    CBS Prediction Servers
   http://www.cbs.dtu.dk/services/
RevTrans, MatrixPlot,RNA Structure Logos
    CBS Bioinformatics Tools
   http://www.cbs.dtu.dk/biotools/
PSIpred, Protein Structure Prediction Server
    http://bioinf.cs.ucl.ac.uk/psipred/
FFAS, Fold&Function Assign System etc. (Burnham Inst.)
   http://bioinformatics.ljcrf.edu/pages/
List of secondary structure prediction sites
   xxx
Mfold RNA secondary structure prediction
   http://bioweb.pasteur.fr/seqanal/interfaces/mfold-simple.html
DALI/Fssp 3D structure search
    http://www.ebi.ac.uk/dali/

Gene prediction
Genscan
   http://genes.mit.edu/GENSCAN.html
HMMGENE
   http://www.cbs.dtu.dk/services/HMMgene/

Multiple Sequence Alignments
ClustalW
   http://npsa-pbil.ibcp.fr/cgi-bin/npsa_automat.pl?page=npsa_clustalw.html
T-coffee
   http://www.ch.embnet.org/software/TCoffee.html

MODEL ORGANISMS

Model organisms, taxonomy & information
NCBI Taxonomy
   http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html
NIH Model organisms for biomedical research
   http://www.nih.gov/science/models/
TIGR Gene Indices   http://www.tigr.org/tdb/tgi/
The Encyclopedia of Life (EOL), complete proteome of all organisms
   http://eol.sdsc.edu/

Model organism databases
Some of the sequencing initiatives on model organisms. Additional information on the progress of numerous model organism sequencing initiatives can be found on the Model Organisms for Biomedical Research web page, at http://www.nih.gov/science/models/. A more extensive list of organismal databases can also be found through the online Nucleic Acids Research Database Collection, at http://nar.oupjournals.org/cgi/content/full/30/1/1/DC1.