This is a small package for extracting contextual information about dual-coding exons highlighted by Mirage2 during intra-species multiple sequence alignment.

When you first download this package, you'll need to run the pseudo-makefile lazy_maker.sh within the hsi subdirectory. Then, you can use the following to run the extractor:

./DCE-Extractor.pl [Mirage2-Results] [Species-Guide]

Where Mirage2-Results is the output directory produced by a run of Mirage2, and Species-Guide is the guide file used to associate species with their genomes during that run of Mirage2.

The results of the extractor will be placed in a directory named Extracted-DCEs/ Within this directory, there will be a CSV-formatted file for each species that lists each collection of left- and right-hand genomic windows of 32 nucleotides (centered around the splice-in and splice-out sites that define the dual-coding region), organized by "groups" within gene families.

In addition to the species-specific CSV files, there is also a subdirectory for each species where the detailed protein-to-genome alignments are depicted.

Finally, there may be a file called Gappy-Sequences.out which lists any sequences for which the mapping of amino acids to the genomic region relevant to a dual-coding region highlighted by Mirage2 is gappy (suggestive of low-quality alignment and less likely to be genuinely dual-coding).