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There are currently plenty of programs available for mapping short sequences(reads) to a genome. Most of them, however, including such popular and activelydeveloped programs as Bowtie, BWA, TopHat and many others, are based onBurrows-Wheeler Transform (BWT) algorithm. This approach is very effective formapping high-homology reads, but runs into problems when mapping reads withhigh level of errors or SNP. Also it has problems with mapping RNASeq splicedreads (such as reads that aligning with gaps corresponding intron sequences),the kind that is essential for finding introns and alternative splicing geneisoforms. Meanwhile, finding intron positions is the most important task fordetermining the gene structure, and especially alternatively spliced variantsof genes. In this paper, we propose a new algorithm that involves hashingreference genome. ReadsMap program, implementing such algorithm, demonstratevery high-accuracy mapping of large number of short reads to one or moregenomic contigs. It is achieved mostly by better alignment of very short partsof reads separated by long introns with accounting information from mappingother reads containing the same intron inserted between bigger blocks.Availability and implementation: ReadsMap is implemented in C. It isincorporated in Fgenesh++ gene identification pipeline and is freely availableto academic users at Softberry web server www.softberry.com.

ReadsMap: a new tool for high precision mapping of DNAseq and RNAseq read sequences