Documentation read from 04/17/2019 22:07:28 version of /vol/public-pseed/FIGdisk/FIG/bin/svr_tmpred_predictions.



Estimate transmembrane domains



    svr_all_features 3702.1 peg | svr_tmpred_predictions

would produce a 5-column table. The first column would contain PEG IDs for genes occurring in genome 3702.1, and the remainder are use to capture the core domains and scores produced by TMpred. There would be a separate line for each predicted TM domain.


The standard input should be a tab-separated table (i.e., each line is a tab-separated set of fields). Normally, the last field in each line would contain the PEG for which functions are being requested. If some other column contains the PEGs, use

    -c N

where N is the column (from 1) that contains the PEG in each case.

This is a pipe command. The input is taken from the standard input, and the output is to the standard output.

Command-Line Options

-c Column

This is used only if the column containing PEGs is not the last.

-min MinSc [defaults to 0]

Output Format

The standard output is a tab-delimited file. It consists of the input file with five extra columns added:

    the beginning of the core domain
    the end of the core domain
    the score
    the predicted center
    the direction (outside-to-inside or inside-to-outside)


Hey! The above document had some coding errors, which are explained below:

Around line 76:

You forgot a '=back' before '=head2'