Input: There are two inputs, (i) a multiple alignment of target motif (model) and (ii) a target proteome (this beta-version does not allow scanning for multiple motifs); further explanation of input formats is provided on top of the dialog box which is displayed after clicking the add button.

Run: Select the input motif and target proteome by left-clicking their respective rows; next select a type of job to run. Either a quick job (i.e. a Viterbi scan) or a precise job (a Viterbi decoding as well as a posterior decoding) can be chosen. The page refreshes automatically and the result will be highlighted. (Note: the quick Viterbi scan usually takes less than 30 seconds for a medium-sized proteome, while the precise one can take a couple of minutes; the page can also be refreshed manually.)

Output: The output is a zipped text file containing the sequence identifier (if FASTA format), assigned motif (residues and their respective positions) and Viterbi log-odds score. For posterior decoding, assigned motif (residues and their respective positions), as well as posterior probabilities are given. (Note: output results can be sorted by score in any spreadsheet application.)

Please send any comments or questions to Pavle Goldstein.

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