computeRT.pl - Compute retention time
./computeRT.pl [--method=METHOD [--saveparam=PARAM] [--current=CURRENT]|[--learnfrom=LEARN] [--settings=SET]] | [--readparam=PARAM] [--calibratefrom=CAL] [--out=OUT] (filein1 [ filein2[...]] | - )
The algorithm to be taken (irrelevant if parameters are to be read from a file). Currently available algorithms are: Hodges(averaged sum of amino acid coefficients), Krokhin (modified Hodges) and Petritis (neural network).
For Hodges algorithm, precomputed coefficients can be chosen among several references in the literature: Guo86 (default), Guo86_2, Meek80, Su81, Krokhin04, Sagasawa82, Meek81, Browne82, Casal96, Meek80_2, Browne82_2, Petritis03.
Output text file (or STDOUT if no such argument is given)
Learn from experimental data in LEARN the coefficients in Hodges algorithm or neural network weights in Petritis. File format of blank-separated columns: "amino acid sequences" "retention time" "additional cols" ...
XML file with additional settings for learning, filtering, etc. See 'rtset.dtd'.
Calibrate the algorithm by fitting some experimental data. Same format than for learning.
Save current params in PARAM, including current coefficients and calibration.
Retrieve current params in PARAM, including current coefficients and calibration.
Print a brief help message and exits.
Print the manual page and exits.
All remaining arguments are names of input files; or '-' for the standard input.
This program will estimate the HPLC retention time for a given list of peptides. Several prediction algorithms can be chosen. It is also possible to train the coefficients used in the algorithm or to calibrate the estimates to a set of experimental values.
To install InSilicoSpectro, copy and paste the appropriate command in to your terminal.
cpanm
cpanm InSilicoSpectro
CPAN shell
perl -MCPAN -e shell install InSilicoSpectro
For more information on module installation, please visit the detailed CPAN module installation guide.