This is the command reprof that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
NAME
reprof - predict protein secondary structure and solvent accessibility
SYNOPSIS
reprof -i [query.blastPsiMat] [OPTIONS]
reprof -i [query.fasta] [OPTIONS]
reprof -i [query.blastPsiMat|query.fasta] --mutations [mutations.txt] [OPTIONS]
DESCRIPTION
Predict protein secondary structure and solvent accessibility.
Output Format
The output format is self-explanatory, i.e. the colums of the output are described in the
output file itself.
OPTIONS
-i, --input=FILE
Input BLAST PSSM matrix file (from Blast -Q option) or input (single) FASTA file.
-o, --out=FILE
Either an output file or a directory. If not provided or a directory, the suffix of
the input filename (i.e. .fasta or .blastPsiMat) is replaced to create an output
filename.
--mutations=[all|FILE]
Either the keyword "all" to predict all possible mutations or a file containing
mutations one per line such as "C12M" for C is mutated to M on position 12:
C30Y
R31W
G48D
This mutation code is also attached to the output filename using "_". An additional
file ending "_ORI" contains the prediction using no evolutionary information even if a
BLAST PSSM matrix was provided.
--modeldir=DIR
Directory where the model and feature files are stored. Default: /usr/share/reprof.
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