Table 4. Features of the available tools for the analysis of coordinate and SNVs.

Software	Time	Peak Memory Usage (MB)	Comments
For Coordinates
CisGenome	12m42s	11.2	• Can select different ranges to consider for upstream and downstream• Single output, no statistics
PeakAnnotator	unknown	33000	The program exceeded the available RAM on our server
Segtor	5m48s	842	• Multiple fixed ranges for upstream and downstream• Various files depending on the biological question
For SNVs
SeqAnt	63m11s	805	• Cannot specify a range parameter for upstream/downstream• Limited number of species
Annovar	3m18s	228	• Fast and memory efficient• Does not provide statistics, reports a single isoform per hit
Sequence Variant Analyzer	120m50s	7700	• Graphical User Interface• Provides greater information at the expense of speed
Segtor	8m58s	1579	• Produces output files and statistics on a per hit, per gene or per isoform basis• Can produce the set of mutated protein sequences

A case study of using the currently available software tools for annotating SNVs and coordinates to characterize genomic position of the 2,707,221 SNVs from the SRX016474 dataset. The corresponding coordinates of the SNVs were used as inputs for the software aimed at annotating coordinates. With the exception of Sequence Variant Analyzer which came with its own pre-compiled set of various gene databases, every tool in the list used RefSeq as source of annotation. These tests were conducted on an server with 8 CPUs at 2.5 GHz and 33 GB of RAM.