BMC Genomics 2007, 8:427 http://www.biomedcentral.com/1471-2164/8/427 FRiegpueraet f5amilies common to P. sativum, G. max and M. truncatula genomes Repeat families common to P. sativum, G. max and M. truncatula genomes. A. Proportion of sequences shared between pea (P. sativum) and soybean (G. max). The graph shows percentage of 454 reads with significant similarity to sequences from the other species. The contribution of various repeat families is displayed in different colors as indicated on the legend. B-D. Repeat families conserved between pea and soybean (B), soybean and M. truncatula (C), and pea and M. truncatula (D). Dots on the scat- ter plots represent 454 reads from one species with similarity to sequences from the other species. Positions of the dots along the axes correspond to the number of significant hits obtained for each 454 read and to their average similarity expressed as BLAST bit score. Repeat families are displayed in the same colors as on panel A; rDNA and unidentified sequences were omitted from panels C and D. workers [32], who aimed at the recovery of ancestral sequences for rice mobile elements from whole genome shotgun sequences. They developed an algorithm based on short oligomer (K-mer) frequency analysis for repeat identification and reconstruction. However, the program implementing this analysis was designed for processing conventional sequence reads of at least several hundred nucleotides in length and could not be adapted to work with the short 454 sequences. Thus, we used a different strategy, employing sequence-similarity based clustering of the reads followed by assembling them into contigs representing reconstructed fragments of the genomic repeats. Although the TGICL program package used to perform this analysis was originally designed for cluster- ing ESTs [25], it provides a number of customizable parameters, which after proper adjustment resulted in the desired performance with our data. It should be noted, however, that even with these settings, most repeats could not be reconstructed as a single contig spanning their full- length sequences and including most of the sequence Page 9 of 16 (page number not for citation purposes)