Chengdu is located at the western edge of the Sichuan Basin and sits on the Chengdu Plain; the dominating terrain is plains. The prefecture ranges in latitude from 30° 05' to 31° 26' N, while its longitude ranges from 102° 54' to 104° 53' E, stretching for 192 kilometers (119 mi) from east to west and 166 km (103 mi) south to north, administering 12,390 km2 (4,780 sq mi) of land. Neighboring prefectures are Deyang (NE), Ziyang (SE), Meishan (S), Ya'an (SW), and the Ngawa Tibetan and Qiang Autonomous Prefecture (N). The urban area, with an elevation of 500 m (1,600 ft), features a few rivers, three of them being the Jin, Fu, and Sha Rivers. Outside of the immediate urban area, the topography becomes more complex: to the east lies the Longquan Mountains (龙泉山脉) and the Penzhong Hills (盆中丘陵); to the west lie the Qionglai Mountains, which rise to 5,364 m (17,598 ft) in Dayi County. The lowest point in Chengdu Prefecture, at 378 m (1,240 ft), lies in the southeast in Jintang County.
Summary: Due to the availability of new sequencing technologies, we are now increasingly interested in sequencing closely related strains of existing finished genomes. Recently a number of de novo and mapping-based assemblers have been developed to produce high quality draft genomes from new sequencing technology reads. New tools are necessary to take contigs from a draft assembly through to a fully contiguated genome sequence. ABACAS is intended as a tool to rapidly contiguate (align, order, orientate), visualize and design primers to close gaps on shotgun assembled contigs based on a reference sequence. The input to ABACAS is a set of contigs which will be aligned to the reference genome, ordered and orientated, visualized in the ACT comparative browser, and optimal primer sequences are automatically generated. Availability and Implementation: ABACAS is implemented in Perl and is freely available for download from Contact: email@example.com PMID:19497936 2b1af7f3a8