Spaln boundary scorer

Tomas Bruna, Alexandre Lomsadze, Mark Borodovsky

Georgia Institute of Technology, Atlanta, Georgia, USA

Reference: GeneMark-EP+: eukaryotic gene prediction with self-training in the space of genes and proteins

Description

Spaln boundary scorer parses introns, starts, stops and exons from Spaln's alignment output and scores them. Introns, starts and stops are scored based on local alignment quality around their boundaries. Detailed description of how the scores are computed is available in https://academic.oup.com/nargab/article/2/2/lqaa026/5836691.

Installation and usage

To install, clone this repository and run make in the root folder.

To run, use the following command:

spaln_boundary_scorer < spaln_input -o output_file -s matrix_file [-w integer] [-k kernel] [-e min_exon_score] [-r]

Input details:

• The program can parse multiple separate alignments saved in the same input.
• The input is read from stdin.
• Each input alignment is assumed to be on a single line (number of characters per line, controlled by -l option in Spaln, is larger than the alignment length).

Available options are:

   -o Where to save output file
   -s Path to amino acid scoring matrix
   -w Width of a scoring window around introns. Default = 10
   -k Specify type of weighting kernel used. Available opti-
      ons are "triangular", "box", "parabolic" and 
      "triweight". Triangular kernel is the default option.
   -e Minimum exon score. Exons with lower scores (and int-
      rons bordering such exons; start and stops inside the 
      exons) are not printed. Default = 25
   -r Process alignments on the reverse DNA strand (which are
      ignored by default)

Tests

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_spaln_boundary_scorer