BETHESDA, Md.--The US National Center for Biotechnology Information (NCBI) has announced the availability of several new features at its web site, http://www.ncbi.nlm.nih.gov.
Organism-specific Blast allows users to limit searches to specific organisms by selecting from a menu of common organisms or by entering an organism name or taxonomic group. A new matrix menu lets users change from the default BLOSUM62 matrix and select gap existence and extension costs. A number of master-slave alignments are also now allowed, in addition to the default pairwise alignment view.
Pattern Hit Initiated Blast (PHI-Blast) is now available for protein queries in version 2.0 of the Blast program suite. Users can input a protein query sequence and a pattern contained in that sequence, then PHI-Blast searches a specified sequence database for other protein sequences that also contain the pattern and have significant similarity to the query sequence in the vicinity of the pattern occurences.
NCBI's 1998 Gene Map provides mapping information and associated data and annotations for 30,181 human gene-based markers. It was produced by a collaboration of 63 scientists from government, university, and commercial laboratories around the world. A companion page, Genes and Diseases, provides information for 60 diseases associated with specific genes and has links to the 1998 Gene Map, as well as to PubMed, protein sequences, Online Mendelian Inheritance in Man, and associations related to each disease.
NCBI has also established, in collaboration with the National Human Genome Research Institute, the dbSNP database to serve as a central repository for single-base nucleotide substitutions and short deletion and insertion polymorphisms. The data in dbSNP will be integrated with other NCBI genomic data and, as with all NCBI projects, will be freely available to the scientific community in a variety of forms.