Alignment Annotator

  cd /home/people/christo/public_html/strap/AA2/tmp/apache/x4bdf54f761_1df8/; less -R stdout.txt
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.

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 running.php which returns the number of jobs in the queue.

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
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
gff http://www.bla.bla/file.gff The gff file lists annotations in GFF format
das t Missing UniProt IDs will be determined prior loading BioDAS annotations.
For controlling the list of DAS services, use the script command DAS_features.
egef t Missing UniProt IDs will be determined prior loading annotations from ExPASy.
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 after loading the sequences but before other comands are run.
script20 -29 http://www.blab.bla/script25.txt URL of a script file which is executed at the end.
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.