Simple Interface to the Kabat Sequence Database
This page provides a simple point-and-click interface to the KabatMan database. This interface only lets you create simple queries; for more complex cases, you must write queries directly using the in the KabatMan SQL-like query language.
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.
25.09.06 LEN() function
The LEN() function can now be used with framework regions as well as CDRs.
24.08.06 New SEQUENCE command
The SEQUENCE command works like PIR but produces a Kabat numbered sequence rather than a PIR file.
You may now use LFR1, LFR2, LFR3, LFR4, HFR1, HFR2, HFR3, HFR4, (in the same way as L1, L2, etc.) to extract the sequences of the 8 framework regions. These may all be used in SELECT or WHERE clauses.
03.04.02 New DATE command
You can now use DATE to extract the year of the earliest publication.
You can now specify the delimiter used between fields in the output. You may also select human subgroups (thanks to Sophie Deret) as has been available from the full query interface for the last year.
There is now a new selection field: subgroup() which takes either L or H as a parameter. This gives the subgroup of either the light or heavy chain. It may be used in SELECT or WHERE clauses. Note that this only works for human sequences.
There is now an option to specify which definition of canonicals you wish to use. The default is pretty much as before (i.e. derived from AbM definitions although additional classes have been removed as they are now covered by the auto mode). The other two modes, strict and auto apply strict definitions from Chothia's papers or my own automated definition of conformation and key residues, respectively.
There are now 4 new selection fields: idlight, idheavy, urllight and urlheavy while allow you to obtain the Kabat accession codes for the light or heavy chain. The url versions return hyper-links to the Kabat Web page; clicking the link will give you the full raw-data entry from their page.
You can now ask for the light chain and heavy chain Kabat accession numbers which are returned as hyperlinks giving you access to the full data from the Kabat Web site.
What information do you wish to display?
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.
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.