Co ordinate Systems used in Afra

• JavaScript and most of the other programming languages uses 0 based indexing and half open intervals. i.,e interval(start, end) is exclusive of the end
• The Feature data and gff files use 1 based indexing.
• A padding of a single is added before every refSeq sequence so that the 1 based indexing of genomic Features can be used with 0 based indexing of JavaScript without any explicit conversion.
• start and end intervals of the genomic Feature data are also half open intervals. This mean the base pair at the end coordinate is not a part of the given feature.