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Orientations and distances of transcribed loci to surrounding annotated genes were extracted from genome annotations of scaffolds using their locations.

Dosage sensitive genes were extracted from the annotations of the Baylor College of Medicine Medical Genetics Laboratory 105k diagnostic Chromosomal Microarray (version 7) [38].

Additional features contain information extracted from genome annotations and from the present analysis.

Information of these sequences, such as subgenotype and recombination, was also extracted from GenBank annotations.

Others functions of the features found in these regions were extracted from RAST annotations.

TSS information was extracted from RefGene annotations downloaded from the UCSC genome browser (https://genome.ucsc.edu/) for version of mm9.

For each concept, GSM can be divided into two groups depending on whether the concept was extracted from their annotations.

For models with repeat features, the content of repeat families as well as individual repeats were extracted from UCSC annotations.

The UTR length, average intron length and protein length for each transcript were also calculated or extracted from the annotations.

In order to find what type of proteins or enzymes possesses identical reverse octapeptide, GO terms of the proteins containing octapeptide pairs (octapeptide and its reverse) were extracted from PDB annotations and stored in appropriate format.

All Leishmania ortholog predictions included in version 2 (29/07/2008) of the L. braziliensis genome that present no more than one ortholog in L. major and L. infantum were extracted from GeneDB annotations [ 8].