We created a new software program for mapping Illumina sequencer reads (MPSmap) and visualizing the mapping results (PSmap). Detailed description and evaluation of the software will appear elsewhere; here, we describe our method briefly. Initially, a simple index of k-mers was prepared for the reference sequence. Then all bases of the read were compared with that of the reference for each index match of the read. This comparison was performed for all the index matches, and the best-matched position for each read was identified. A limitation of the index approach is that some of the close-match positions may not be identified if any mismatches are present within the index. To minimize this problem, we repeated the index search while shifting the index position on read sequences. For instance, we repeated the index search three times to correctly locate the read positions while allowing two mismatches. Similarly, we repeated the index search (n + 1) times, where n is the number of mismatches per read allowed in the search. Each index hit is aligned on the reference in order to look for the best location, allowing up to the specified number of mismatches without a gap. The index approach is fast but does not guarantee sensitivity for reads shorter than k (n + 1), where, k is the index length. For the mapping of B. subtilis allowing 35 mismatches, we compared searches with index lengths of k = 2 and k = 10 in order to confirm that the difference in results is small (Supplementary Table S1). We also performed mapping with BWA and BFAST using Tablet (29 (link)) for visualization, in order to confirm that multiple mapping algorithms detect the SSE (Supplementary Data S1). The visualization program (PSmap) converts the mapping results to a PostScript file. The programs, executable on Linux (CentOS5.3) and MacOSX (ver. 10.6.6) systems, are available for download on our website (http://metalmine.naist.jp/maps/).