Entrez Genomes
IgBLAST
IgBLAST: An Immunoglobulin-Specific Search Tool
Immunoglobulin BLAST (IgBLAST), a specialized variant of BLAST that is designed for the analysis of human or mouse immunoglobulin sequence data, is now available online from NCBI. IgBLAST performs blastn or blastp searches of a non-redundant (nr) database of germline V genes and returns the best three V-gene matches, and the best two D-gene and J-gene matches. IgBLAST also annotates the query sequence, based on the domain information drawn from an alignment between the top-matched germline V gene and the query sequence, using the nomenclature of the Kabat Database of Sequences of Proteins of Immunological Interest. Such features as framework regions (FWR1, for instance) or complementarity-determining regions (CDR1, for instance) are delineated.
IgBLAST may also be used to search the standard BLAST nr database. In this case, the best matches to the germline gene database are aligned with the query as before, followed by the best hits to the nr database. One additional feature of IgBLAST is its ability to flag the returned matches from the nr database according to their germline V-gene origins. This allows one to distinguish easily between the results that use the same germline V-gene as the query and those that do not.
Although IgBLAST also supports protein searches using blastp, only V-gene matches will be reported. D-gene and J-gene matches are reported only for DNA searches with blastn.
The germline V-gene database currently contains Igh, Ig kappa, Ig lambda, and D and J genes from both human and mouse. The database can be viewed in the form of an annotated multiple sequence alignment by clicking on the appropriate database link in the sidebar of the IgBLAST page.
Try IgBLAST at www.ncbi.nlm.nih.gov/igblast.—DW, JY
