1998

10/19	Organism-specific BLAST	Organism-specific BLAST is now available at the NCBI. Users may limit their BLAST search to a specific organism selected from a pull-down menu of common organisms or by entering an organism name (Genus species) or a taxonomic group (e.g.,"Eubacteria"). A new matrix menu allows users to easily 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. All of these options can be selected from the Advanced BLAST page.
10/09	Chromosomal Breakpoints in Human Cancer	This version of a recent special issue of Nature Genetics (Nat Genet 1997 Apr;15 Spec No:417-74) provides access to the breakpoint map of recurrent chromosomal rearrangements in human neoplasia. Access to this map, constructed by Mitelman et al., is via a summary table, chromosome ideograms, and a query = function.
10/02	1998 Gene Map; Genes and Disease	The 1998 version of NCBI's Gene Map provides the mapping information and associated data and annotations for 30,181 human gene-based markers. The 1998 Gene Map was produced by a collaboration of 63 scientists from government, university, and commercial laboratories around the world; an accompanying paper will be published in the Genomes issue of Science in late October.   A companion page, Genes and disease, provides information for some 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.
09/29	PHI-BLAST	A new service called Pattern Hit Initiated BLAST, or PHI-BLAST, is now available in Version 2.0 of the BLAST program suite. Currently, PHI-BLAST may be used only for protein queries. PHI-BLAST expects as input a protein query sequence and a pattern contained in that sequence. PHI-BLAST searches whatever sequence database is specified for other protein sequences that also contain the input pattern and have significant similarity to the query sequence in the vicinity of the pattern occurrences. Patterns are specified using PROSITE syntax as explained in the documentation. Statistical significance is reported using E-values as for other forms of BLAST, but the statistical method for computing the E-values is different. PHI-BLAST is integrated with Position-Specific Iterated BLAST (PSI-BLAST), so that the results of a PHI-BLAST query can be used to initiate one or more rounds of PSI-BLAST searching. PHI-BLAST is under development and may change substantially over time.
09/17	dbSNP: A Database of Human Genetic Variation	The NCBI database of human genetic variation is now available in dbSNP. This site provides user interfaces for browsing and querying the database and instructions for submitting new mutations to the database. dbSNP contains both the experimental conditions used to find each mutation and each mutation's observed variation for populations and individuals. dbSNP entries include single nucleotide polymorphisms (SNPs), small-scale insertion/deletions, and polymorphic repetitive elements and will soon contain microsatellite variation. This information will be useful for physical mapping, disease association, and surveys of population structure.
09/17	Version 2 of Cn3D Visualization Tool	A new version of Cn3D has been released, which features simultaneous display of biomolecular structures and their sequences. Precalculated protein structure superpositions can be shown in 3D and as sequence alignments. You can use Cn3D to highlight sequence regions in 3D, to import and align sequences of interest, and learn about structural properties via homologous representatives.
08/01	Subtyping HIV-1 Sequences	A new tool that uses the BLAST algorithm to identify the subtype of an HIV-1 query sequence is now available. This program detects the best local similarities between a query sequence and a set of HIV-1 subtype reference sequences. A sliding window along the query sequence allows the detection of possible intergenic recombinants with interspersed genetic regions from two or more subtypes.
07/15	New Batch Entrez Feature	Batch Entrez now allows a search query to be used for retrieving a large set of sequences to a local disk file. Retrievals can also be based on a list of accession/GI numbers or a specific organism.
05/04	Unfinished Microbial Genomes	A BLAST page for searching sequences from various unfinished microbial genomes is now available. These incomplete genome sequences are not yet available in GenBank or Entrez. Queries can be done on all or a subset of the unfinished microbial genomes simultaneously via TBLASTN, BLASTN, or TBLASTX.
03/05	Human Genome Sequencing Index (HGSI)	The Human Genome Sequencing Index (HGSI) is a joint project between the NCBI and the Human Genome Organization (HUGO) to track the sequencing efforts of the Human Genome Project. HGSI provides tables and graphic displays of the regions of the genome targeted by various sequencing centers. Sequencing centers may directly submit and update their target data using Web forms.
01/26	PubMed 2.0 Now Available	Several features have been added to PubMed, including new searching capabilities, a document ordering system (Loansome Doc), and a browser for the MeSH indexing vocabulary.

Revised: June 6, 2002.