GeneIndex: An Open Source Parallel Program for Enumerating and Locating Words in a Genome

GeneIndex is an open-source program that locates words of any length k specified by the user in a sequence. GeneIndex is useful for understanding the structure of entire genomes or very large sets of genetic sequences, particularly in finding highly repeated words and words that occur with low frequency. GeneIndex accepts DNA sequences in FASTA format input files, and performs computations and input/output in parallel. GeneIndex has been implemented on Linux, IBM AIX, and NEC SX-8, and is available with test data sets (the entire genomes of Drosophila melanogaster and Homo sapiens). The performance of the program scales well with processor count -- that is, as the number of processors increases, the processing time required decreases proportionally.