Alignment Annotator

Author: christoph.gille charite.de   Institut für Biochemie, Charité, Berlin

Programming Interface

Alignment Annotator can be linked into other Bioinformatics services. Try the link PFAM:PF06446 and look at the URL: 
http://www.bioinformatics.org/strap/aa/aa.php?sequences=http%3A%2F%2Fpfam.sanger.ac.uk%2Ffamily%2Falignment%2Fdownload%2Fgzipped%3Facc%3DPF06446%26alnType%3Dfull%26.gz&egff=t&d3=t&w=70
Please note that the values are URL encoded. The following table lists the web variables. The variable "caller" and either the variable "sequences" must be set. All other variables are not mandatory. Both, HTTP-POST and HTTP-GET are supported.



Variable Example value Description
sequences http://pfam.sanger.ac.uk/family/alignment/download/gzipped?acc=PF06446&alnType=full&.gz An URL of an multiple Fasta file or sequence file or an alignement in e.g. Clustal or fasta format. In case of gzip compression, URLs must end with .gz.
caller my-bioinformatics-tool admin@my-bioinformatics-tool.org The web service name and an Email address to contact.
w 70 The number of residues and gaps per line
d3 t Find homologous 3D files.
For more control use script command project_coordinates
script1 -9 http://www.blab.bla/script5.txt URL of a script file which is executed early.
script20 -29 http://www.blab.bla/script25.txt URL of a script file which is executed late.
send http://www.server/path/ Upload alignment URL where the completed html-document with the alignment file can be sent to. The URL can optionally be followed by a label text. Try it

Load balancing (Under construction)

There will be different mirrors listed in http://www.bioinformatics.org/strap/aa/mirrors.txt. The availability of each service can be checked with the script available.php which returns the number of jobs in the queue or "f".

... I am still working on it.

Obtaining the server side software

The PHP software can be requested from the author.