BAC End Pairs Track Settings
 
BAC End Pairs   (All Mapping and Sequencing tracks)

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Data last updated at UCSC: 2006-08-18

Description

Bacterial artificial chromosomes (BACs) are a key part of many large-scale sequencing projects. A BAC typically consists of 50 - 300 kb of DNA. During the early phase of a sequencing project, it is common to sequence a single read (approximately 500 bases) off each end of a large number of BACs. Later on in the project, these BAC end reads can be mapped to the genome sequence.

This track shows these mappings in cases where both ends could be mapped. These BAC end pairs can be useful for validating the assembly over relatively long ranges. In some cases, the BACs are useful biological reagents. This track can also be used for determining which BAC contains a given gene, useful information for certain wet lab experiments.

The RPCI-98 and DrosBAC libraries, individual clones, and hybridization filters are available from the BACPAC Resources Center (BPRC) at Children's Hospital Oakland Research Institute (CHORI). Individual clones from the RPCI-98 library are named BACR01A01 - BACR48H12 (96-well format; R stands for EcoRI). Individual clones from the DrosBAC library are named BACN01A01 - BACN47H12 and BACH48A01 - BACH61H12 (N stands for NdeII; H stands for HinDIII).

In order to be included in this track, a valid pair of BAC end sequence alignments must be at least 25 kb but no more than 500 kb away from each other. The orientation of the first BAC end sequence must be "+" and the orientation of the second BAC end sequence must be "-".

The scoring scheme used for this annotation assigns 1000 to an alignment when the BAC end pair aligns to only one location in the genome (after filtering). When a BAC end pair or clone aligns to multiple locations, the score is calculated as 1500/(number of alignments).

Methods

BAC end sequences were downloaded from Genoscope (http://jacob.cea.fr/drf/ifrancoisjacob/english/Pages/Departments/Genoscope/Genoscope_s-bioinformatics-resources.aspx) and then placed on the assembled sequence using Jim Kent's blat program. Terry Furey's pslPairs program was used to identify paired end alignments.

Credits

The RPCI-98 BAC library was produced by BACPAC Resources, then at Roswell Park Cancer Institute and now at CHORI, in collaboration with the Berkeley Drosophila Genome Project. The DrosBAC library was made by Alain Billaud at CEPH (Centre d'Etude du Polymorphisme Humain) in a collaboration with the European Drosophila Genome Project co-ordinated by D. Glover. Thanks to Genoscope for providing the BAC end sequence files.