• What is the guideline for submitting igblast searches via scripting?
  
  1. You should submit multiple query sequences in one submission rather than submitting one at a time. This minimizes hitting our servers too frequently. However you must limit the number of sequences to 500 in each submission.
  
  2. Submit only one batch of searches at a time. You should wait for the result to come back before submitting another batch. You may be blocked from the site if you put too much load on the servers at one time.
  
  You can use our sample scripts to submit batch searches.
  
  
• How do I analyze sequences that are expected to have weak matches? For example my sequences are short or have severe mutations (including deletions and insertions).
  
  You need to choose a larger "Expect" value (such as 1 or 10000) and a lower mismatch penalty (such as -1).
  
  
• What kind of query sequences can be used for IgBlast?
  
  IgBlast is designed to analyze the V, D and J elements of an Ig sequence. However, the query sequence must contain some part of the V (variable) region. This implies that if the query sequence only contains D or J region, it will not be properly analyzed by IgBlast.
  
  
• Which database should I use to find the closest germline V genes?
  
  In general, you can choose the Ig germline V genes database. However, if you want the most stringent search, then you may need to choose Ig V gene sequence or nr database (The "Focus on the V gene segment" option is also recommended for such case, see explanation). There are two reasons for this. First, as sequences in Ig germline V gene database are manually collected from literature, there is a possibility that we might have missed some germline genes; Second, the nr or Ig V gene sequences database includes other sequence records such as genomic sequences from various genome projects and unpublished data that may contain previously unidentified germline genes. When you choose the Ig V gene or nr database, IgBlast will also automatically search the Ig germline gene database and report the top three germline hits (As a result, you will not miss anything if you are only interested in finding the top germline matches).
  
  
• How often do you update the databases?
  
  We update the nr, pdb and Ig V gene sequence databases daily. The germline gene database is updated whenever we are aware of new published germline genes. For germline genes imported from other sources (such as human germline genes from IMGT), we check the source database daily to keep our data in sync.
  
  
• What if my germline V gene is not in your database?
  
  If you know a germline V gene sequence is not in our Ig germline V genes database, you can put it in "Use your own germline V gene" box on IgBlast page and the result will list your germline sequence as top hit. Better yet, you can notify blast-help@ncbi.nlm.nih.gov and we'll be happy to add it to our germline gene database (as long as the sequence has been published). IgBlast can only become a better resource with input from immunology community.
  
  
• What is the difference between Ig V gene sequence database and the nr database?
  
  Ig V gene sequence database is a subset of the nr and the patent database. It essentially includes all human and mouse Ig V gene sequences that have significant length, except that sequences with gross defects (i.e., those with major insertion or deletion in some rare cases) might have been excluded. See our selection criteria for details. Choose this database if you are only interested in human or mouse Ig V gene sequences because the search speed is faster.

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Last modified: Fri Sep 16 13:02:35 EDT 2011