Select the numbering scheme:
Output:
Apply numbering from your scripts
You may also access the numbering program directly from your scripts using our simple REST-style web-services interface.
Numbering sequences
To number a sequence use a URL of the form:http://www.bioinf.org.uk/abs/abnum/abnum.cgi?plain=1&aaseq=sss&scheme=xxx
The fields in the URL are as follows:
Field Meaning plain=1 This causes the CGI script to generate plain parsable text rather than HTML aaseq=sss sss is the amino acid sequence scheme=xxx xxx is the numbering scheme (-k = Kabat, -c = Chothia, -m = Martin)
You can download a sample Perl script that uses the web services-interface to Abnum.
Numbering structures
To number a structure you must pass parameters in POST format and use enctype="multipart/form-data" . The URL is:http://www.bioinf.org.uk/abs/abnum/abnumpdb.cgi
The fields in the URL are as follows:
Field Meaning plain=1 This causes the CGI script to generate plain parsable text rather than HTML pdb=ccc ccc is the coordinate file name output=ooo ooo is output type (-l = relabel as chains A,B,C,D, etc) scheme=xxx xxx is the numbering scheme (-k = Kabat, -c = Chothia, -m = Martin)
The numbering program was written by Abhinandan K. Raghavan,
2006-7. For more information, or if you publish work which has
used this server, please see Abhinandan, K.R. and Martin,
A.C.R. (2008) Analysis
and improvements to Kabat and structurally correct numbering of
antibody variable domains Molecular
Immunology , 45 ,
3832-3839. [PDF
as submitted ]
[http://dx.doi.org/10.1016/j.molimm.2008年05月02日2 ]
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 .