Gene sequence databases

ExPASy (Expert Protein Analysis System, www.expasy.ch) or the National Centre for Biotechnology Information (NCBI, www.ncbi.nlm.gov) websites. Both websites provide bioinformatics tools, links to sequence databases and extensive bibliographic resources. As an example of the wealth of information available on individual enzymes, at the time of writing a search based on nitrilase in the Entrez protein section of NCBI will recover more than 10000 references to nitrilase enzyme amino acid sequences. These can be rapidly screened online by organism, and the individual entries will have links to amino acid and gene sequence, relevant literature and information on protein features (such as conserved domains). 

HGS was among the first biotechnology companies to mine large databases of human gene sequences, looking for previously unknown proteins that might have therapeutic value. Rather than attempting to spell out every letter of DNAs code. 

The x,y,z coordinates of all atoms in published, refined three-dimensional structures have been deposited in the Protein Data Bank (Table 3-4).568 571 Many other related databases are available,572 e.g., covering molecular modeling,573 gene sequences, proteome data,574 and much, much more. A good way to keep up to date is to read the "computer comer" in Trends in Biochemical Sciences (TIBS). Most databases can be reached on the World Wide Web.572 A selected list is... 

Searches for similar protein and nucleic acid sequences Protein structures on moving 3D coordinates Sequence retrieval system for cross-referencing databases Searches for similar protein sequences Database of gene sequences... 

BLAST Chime Entrez (NCBI) FASTA GenBank (NCBI) Molecules R Us RasMol (Ras Mac) SRS (EMBL) Searches for similar protein and nucleic acid sequences Protein structures on moving 3D coordinates Sequence retrieval system for cross-referencing databases Searches for similar protein sequences Database of gene sequences Provides coordinates for protein 3D structure and manipulation Provides coordinates for protein 3D structure and manipulation Sequence retrieval system for cross referencing databases... 

In fact, comparison of EST-translated sequences with all other gene sequences from other species available in the public databases showed that... 

EST databases contain sequence data on cDNA sequences, from a number of organisms, made from single random passes. There are millions of ESTs within these databases and although, commonly, they only cover a small section of organisms, genes and proteins, they are still valuable in the identification of proteins (Andersen and Mann, 2000). However, more recent EST projects are believed to cover a greater proportion of an organism s transcriptome. 

From genome sequences, a plethora of DNA sequence information is, often publicly, accessible in databases. Pieces of genome sequence have often been annotated, based on sequence similarity to other genes with similar function, to possess a certain function. From the gene sequence, the corresponding protein sequence of a putative enzyme can of course be readily derived so that at this stage the target of the search for a new enzyme is defined. 

Accession number ] [Gene sequence] Alignment Modelling Secondary structure Figure 14.3 Information about an enzyme (e g., leucine dehydrogenase, LeuDH) in the databases. 

Bioinformatics uses computers to create and maintain large electronic databases on genomes, protein sequences, and proteomes. With the help of protein prediction software, the computer analysis of genome sequences is producing thousands of new proteins of unknown structure and function. These proteins are called hypothetical proteins because they are predicted from the gene sequence. To know if they really exist would require that they be isolated, purified, and subjected to X-ray crystallography or... 

CRITICAL ASSESSMENT OF THE METHOD Since MS instrumentations today are robust and sensitive, protein identification by PMF is quite good. The rapid development of protein and gene sequence databases provides an ever more consistent platform for searches. Furthermore, improvements in search algorithms and the application of sophisticated statistical methods has improved the reliability... 

A large number of sequence analyses must be performed in order to build a statistically relevant database of sequence variation versus phenotype for a given gene or set of genes.22 For example, patterns of mutation in certain genes confer resistance to HIV for various antiretrovirals. Sequence analyses... 

---