INTROnSPECTIVE and NORA: computerized compositional characterization of regions within introns and around start codons on the basis of non-randomness analysis

Non-randomness analysis has recently proven a valuable method in the characterization of chromosomes and genomes with respect to the nucleotides around start codons. This methodology has been implemented in a distributable program NORA, which is presented as freeware for users in academia. Moreover, because the current knowledge about introns is limited, another application, INTROnSPECTIVE, has been developed. This application analyzes introns in either direction (from 5′ to 3′ or from 3′ to 5′) and the user has the option to exclude introns on the basis of their size or intron number within the gene. Both programs are based on initial parsing of GenBank flatfiles, i.e., with these programs, entire genomes or chromosomes can be parsed and characterized within seconds. The programs run under 32-bit Windows operating systems and can be obtained via http://www.dfuni.dk/~anfu/Bioinformatics/Main.htm. They are the only ones available which perform non-randomness analysis, and INTROnSPECTIVE represents a comprehensive and novel methodology for the study of introns.