BMC Genomics 2006, 7:283 http://www.biomedcentral.com/1471-2164/7/283 BFoigvuGreen5RH map of BTA 5 compared with MARC 2004 (far left), Btau_2.0 (left), and the ILTX 2005 map (right) BovGen RH map of BTA 5 compared with MARC 2004 (far left), Btau_2.0 (left), and the ILTX 2005 map (right). Only labels of corresponding markers of the MARC 2004 and ILTX 2005 map are displayed. Lines between the maps connect common markers. Correspondences of consistently ordered markers included in Btau_2.0 and BovGen RH are high- lighted by dark blue. Red dashes represent corresponding marker positions, black dashes non-corresponding positions. Dis- tances on the Btau_2.0 are scaled in Mbp. Distances on Btau_2.0 are scaled in Mbp, on the BovGen RH map in cR, on the MARC 2004 map in cM and on the ILTX 2005 map in TSP. result there are fewer correspondences of our map with ILTX 2005 than with the old ILTX 2004. It can be assumed that this process improved the ILTX map enormously. Therefore, we used the ILTX 2005 map for comparison despite fewer correspondences. Nevertheless, the ILTX 2004 map has a similarly high marker order consistency and chromosomal assignment with the BovGen RH map (data not shown). Comparison with the sequence assembly Sequence similarity search algorithms used to align maps with Btau_2.0 have a considerable risk of errors as they may also detect gene duplications or similar motifs in dif- ferent genes. To minimize this problem we used very strin- gent parameters for minimum homology and maximized the required length of overlap between sequences. In addition, sequence matches were assessed manually. Thus the loci we aligned between the different maps and the bovine sequence carry a very high probability of correctly assigned homology. Differences in the position of indi- vidual markers between different maps could be the result of technical variations explained by using different parameters and algorithms to construct the multipoint maps. Inconsistencies in the chromosomal assignment of individual markers may also have simple explanations, such as poor primer design resulting in amplification of Page 10 of 15 (page number not for citation purposes)