reprof1
Predict protein secondary structure and solvent accessibility
Usage
reprof -i
[query.blastPsiMat]
[OPTIONS]
reprof -i
[query.fasta]
[OPTIONS]
reprof -i
[{query.blastPsiMat | query.fasta}]
--mutations
[mutations.txt]
[OPTIONS]
Overview
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:
C30YR31WG48DThis 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.
Examples
- Prediction from BLAST PSSM matrix for best results:
-
reprof -i /usr/share/doc/reprof/examples/example.Q -o /tmp/example.Q.reprof
- Prediction from FASTA file:
-
reprof -i /usr/share/doc/reprof/examples/example.fasta -o /tmp/example.fasta.reprof
- Prediction from BLAST PSSM matrix file using the mutation mode:
-
reprof -i /usr/share/doc/reprof/examples/example.Q -o /tmp/mutations_example.Q.reprof --mutations /usr/share/doc/reprof/examples/mutations.txt# Result files for the above call are going to be:# /tmp/mutations_example.Q.{reprof,reprof_F172P,reprof_M1Q,reprof_N34Y,reprof_ORI} - see --mutations for a description of the extensions.
Releases
7 releases since Debian 7 (Wheezy); the text changed 5 times.