This page introduces the concepts used and methods provided by the P-Type ATPase Toolbox. The features available are:
The classification methods both take a FASTA formatted file as input. The annotated version of UniProt is browsable through an easy-to-use interface which allows for filtering of the entries and easy extraction of the results.
The FASTA format is the most widely used format for storing sequences. Below, an example of a FASTA file is shown.
>header of the first entry ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT >header of the second entry TGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCA
Each line beginning with a
> signifies a new entry in the file.
The text following the
> is arbitrary and can thus contain e.g.
the accession id of the entry or some information about the sequence belonging
to the entry.
A FASTA formatted file must be saved as plain-text using e.g. Notepad.
Common extensions are
Once you have created or obtained a FASTA file with P-Type ATPase sequences which you want to know the sub-type of, copy-and-paste the contents of the file (which must be opened in e.g. Notepad) into the text area on the classification page
We provide access to two different classification methods. The main method based on k-nearest neighbors is described in  which provides the best classification accuracy, while the secondary method is based on a method described in , which is faster, but provides a lower classification accuracy. We therefore recommend the use of the main method, unless speed is essential.
When a classification job has been submitted it will run as soon as resources are available and the results will be shown. The query sequences are shown grouped by their predicted subtype.
A plot is generated showing the number of sequences predicted to belong to each subtype. Clicking a bar of a specific subtype in the plot will scroll to the results for that subtype.
The results can be downloaded as a comma-separated file which can be opened with Excel or any other spreadsheet program for further analysis.
The database made available by PATBox is a resource for exploratory research and discovery of P-Type ATPases. The database is constructed from the UniProtKB database through the following steps:
Questions, comments, feature requests, and bug reports are very welcome and should be directed to Dan Søndergaard at firstname.lastname@example.org.