Tomas Bruna, Alexandre Lomsadze, Mark Borodovsky
Georgia Institute of Technology, Atlanta, Georgia, USA
Reference: GeneMark-EP and -EP+: automatic eukaryotic gene prediction supported by spliced aligned proteins (paper in preparation, 2019)
ProSplign boundary scorer parses introns from ProSplign's alignment output and scores them. Introns are scored based on local alignment quality around their boundaries. Detailed description of how the scores are computed is available in (TODO: add link to manuscript)
To install, clone this repository and run make in the root folder.
To run, use the following command:
prosplign_intron_scorer -i input_file -o output_file [-w integer] [-am] [-s matrix_file] [-k kernel]
The program can parse multiple separate alignments saved in the same input.
Available options are:
-i Path to input file.
-o Where to save output file.
-w Width of a scoring window around introns.
-a Print all introns. Without this flag, only introns
with canonical splite sites and perfectly scored in-
trons with GC-AG and AT-AC splice sites are printed.
-m Multiply partial scores from the left and right boun-
daries of the intron. Default behavior is to sum the
scores from both sides.
-s Use specified scoring matrix for intron scoring. Wi-
thout this option, amino acid scores are determined
based on the quality indicator in the input alignment
file.
-k Specify type of weighting kernel used. Available opti-
ons are "triangular", "linear", "parabolic" and
"triweight". Triangular kernel is the default option.
Unit tests are located in the test folder. To compile a test binary, run
make test in the root folder. Subsequently, run the test binary to evaluate
the tests:
make test
test/t_prosplign_intron_scorer