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How to use PlasMit

PlasMit is a neural network written in C, but for your convenience it posesses a CGI-interface so you can use it via a web form.

Input format
First of all, make sure that your sequences are in amino acid FASTA format. A description of this format can be found at http://www.ncbi.nlm.nih.gov/BLAST/fasta.html. Please note that X (any amino acid), * (translation stop) and - (gap) may be part of your sequence, but will be neglected. In short, this format consists of alternating lines, one starting with a right-arrow ">" indicating the name of the following sequence, and seperated by return (or "\n") the sequence itself, in one letter amino acid code. Only the first 24 N-terminal amino acids will be considered, so there is no need to use longer sequences, but make sure your sequences have at least this length.

Choosing the right output format
Actually, PlasMit is not just one neural network, it's rather four of them. There are two networks based on the amino acid composition, one stringent and one more lax one. And there are two networks based on physicochemical properties, again one stringent one and one lax one. (For details see the description at the technical information page). If you just want to have a single prediction from a jury that evaluated the output of all four networks, choose the "prediction only" option. If you want seperate output of all of the networks, choose the "short output" option. If you also want to have the input vectors of the network, i.e. the amino acid composition and the physicochemical properties' values, choose "extended output".

Uploading your file
Either copy & paste your sequence in the form or upload a plain text file via the file upload button. Note that in case there is something written in the form and you upload a file at the same time, the file upload will be neglected and only the form data will be used. If you pasted sequences to be checked into the form or chose an appropriate file, just press the "Send data / Upload file" button at the bottom of the page.

Problems?
If there remain further problems, please consult the Contact page.