Query the Kabat sequence database - Full query language
This page allows you to query the Kabat antibody sequence database using an SQL-like query language. The main deviation between the language used here and SQL is that clauses within the WHERE statement are combined in reverse polish notation. Also, since there is only one table in the database, there is no FROM statement.
Unless you are asking complex queries, you will probably find the simple point-and-click interface to KabatMan easier!. This only allows you to ask fairly simple queries, but covers the majority of types of queries which people ask. To ask more complex queries, you must use the KabatMan Query Language directly using the text entry box below.
News...
05.12.11 Data reading
A small number of sequences with insertions (e.g. 18D-6 light chain, ID 007779) were not being read correctly as the Kabat format was inconsistent. This is now fixed.
The error reporting done by KabatMan is rather poor at present; if you ask a meaningless question, KabatMan is most likely to ignore you alltogether rather than giving you a sensible error message!
Please read the documentation which covers all you need to know to use the interface.
You can also read the full documentation for the stand-alone version of KabatMan.
In brief, the syntax is:
SELECT column[,column]
WHERE column comparison property
[column comparison property boolop]
column is a column name in the database
comparison is one of: =, !=, <, >,
≤, ≥, includes
property is something you are trying to match in the column
boolop is one of: and, or
Note, in particular,
- Just entering a sequence will not give you any results!
- Spaces must be used around all operators. e.g. you must use RES(L23) = C rather than RES(L23)=C
- If you wish to search for strings containing spaces (e.g. in the antigen field), you must enclose the whole string in inverted commas (double or single).
- If you are comparing strings, you are probably best using the INCludes comparison operator rather than using = for an exact match
- If you are searching for a sequence, you should use amino acid 1-letter code with no spaces. See the manual!
Statistics on the information stored in the Kabat database.
Please note, there was a bug in V2.7-V2.9 in doing substring searches (e.g. for a sequence fragment). This is now fixed.
Please cite the following reference in any publications resulting from searches using this software:
Martin, A.C.R. Accessing the Kabat Antibody Sequence Database by Computer PROTEINS: Structure, Function and Genetics, 25 (1996), 130-133.
Commercial Use
Companies may use this public server, but need to be aware that data are not encrypted and it is not secure.
After trialing the system, companies should consider abYsis. A commercial licence will enable you to install a local version of this code together with an integrated database which can also store and analyse proprietary sequence and structure data.
For information on commercial licences, please contact the distributor Ebisu.