There is a frequent need to apply the same set of prediction and annotation tools to a large batch of sequences. Such tools may reside locally or on remote servers accessed over the web. In order to create a meta-tool able to dispatch one or more sequences to assorted annotation/prediction services it is necessary to define a consistent format for the data required by such services and for the annotations which they provide.
We have determined that the output can be described using one of 6 forms of data: numeric or textual annotation of residues, domains (residue ranges) or whole sequences. A tool may produce a combination of such outputs. With this in mind, an XML data-type definition (DTD) was designed to store the output of any server ('Automated Protein Annotation Tool Markup Language', APATML).
APAT lets you write simple wrappers for annotation servers which then generate APATML as output. Our display program will then format that as HTML (including colouring of residues and graphs) for you to view, or you may write your own programs to extract and analyze the data.
A paper is available describing the system has been published in Bioinformatics, 22,291-296.
APAT was written by PhD student S.V.V. Deevi funded by The Felix Trust at Reading University.
APAT currently provides wrappers for:
- NetPhos http://www.cbs.dtu.dk/services/NetPhos/
- PsiPred http://bioinf.cs.ucl.ac.uk/psipred/ (running locally)
- TargetP http://www.cbs.dtu.dk/services/TargetP/
- TMHMM http://www.cbs.dtu.dk/services/TMHMM/
- ChloroP http://www.cbs.dtu.dk/services/ChloroP/
- NetOGlyc http://www.cbs.dtu.dk/services/NetOGlyc/
- DAS-TMfilter http://www.enzim.hu/DAS/DAS.html
- PrositeScan ftp://us.expasy.org/databases/prosite/tools/ps_scan/ (running locally)
- Plasmit http://gecco.org.chemie.uni-frankfurt.de/plasmit/
- PSort http://psort.nibb.ac.jp/form.html
- SubLoc http://www.bioinfo.tsinghua.edu.cn/SubLoc/
APAT needs some attention after not being updated since 2004. The current version appears not to be working! If you wish to contribute and make the necessary fixes, please access the GitHub page.