- Is there a reference for IgBLAST?
Yes you can find more details on IgBLAST in our published paper Nucleic Acids Res (2013) .
- How do I get stand-alone IgBLAST?
You can get pre-compiled IgBLAST on IgBLAST ftp site. You can get the source files to compile your own IgBLAST program if there is no pre-compiled IgBLAST for your platform.
- How do I save my search parameters and re-use them later?
Click the "Save search parameters" link on IgBLAST search page and then click "OK" button on the pop-up message window. Then bookmark the current page. Now you can click the bookmarked page to re-use the saved parameters for future IgBLAST search.
- What kind of query sequences can be used for IgBlast?
IgBlast is designed to analyze the V (variable) domain sequence. The query sequence must contain some part of the V gene. This implies that if the query sequence only contains D or J gene, it will not be properly analyzed by IgBlast.
- Which database should I use to find the closest germline V genes?
In most cases, searching the germline gene databases is sufficient. However, if you want the most stringent search, consider adding additional database such as nr or genome database. There are two reasons for this. First, as sequences in germline gene database are manually collected from literature, there is a possibility that some germline genes are missed; Second, nr or genome database includes sequences from various genome projects and unpublished data that may contain previously unidentified germline genes.
- How often do you update the germline databases?
The NCBI germline gene collection is updated whenever we are aware of new published germline genes. For germline gene databases from other sources (such as IMGT), we check the source database daily to keep our data in sync.
Last modified: Mon Sep 9 11:07:23 EDT 2013