DNA sequences databases

Oliveira, C. and Johnston, D.A. (2001) Mining the schistosome DNA sequence database. Trends in... 

DNA sequence databases and gene prediction algorithms is still warranted (70). 

The National Center for Biotechnology Information (NCBI). Located at the National Library of Medicine in Bethesda, MD, USA. The home of the GenBank DNA sequence database PubMed literature search engine sequence search tools (e.g., PSI-BLAST) genomic sequence navigation tools. A substantial repository of resources in all areas of bioinformatics. 

The first databases to appear were DNA sequence databases, namely those from the EMBL (Europe), NCBI (USA) and the DDBJ (Japan), known as EMBL [30], GENBANK [18] and DDBJ [1] respectively. These are DNA databases of sequences and their annotations. These databases continue as a collaborative effort, with the three databases sharing their information. So all three databases contain identical data, albeit in a different format. 

Protein databases (e.g., SWISS-PROT and PIR) are almost entirely populated by protein sequences present in DNA sequence database records. 

GenBank Release Notes Genetic codes used in DNA sequence databases HTGS ORF Finder Sequin... 

However, there remain important considerations in the MS analysis of peptides, as compared to those of proteins. These include the fact that the number of specific internal proteolytic (tryptic) sites are limiting and hence generally not available to produce specific peptide fragments. In this regard, MS analysis of proteins has relied heavily on the DNA sequence databases produced from both the genomic and the bioinformatic efforts to predict digested protein fragments. Peptides may be present in many different forms from their mature precursors, to partially processed precursors, to their fully... 

Until recently, phytochromes were thought to be restricted to photosynthetic organisms. -" However, recent studies based on DNA sequencing databases uncovered many phytochrome-like genes in prokaryotic organisms, such as Synechocystis, Bradyrhizobium, and Ddnicoccus. Protein sequence comparison shows that the chromophore bearing N-terminal domains are conserved in all known phytochromes. 

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