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 in the project, these BAC end reads are mapped to the genome sequence. A valid pair of BAC end sequences must be at least 25 kb but no more than 350 kb away from each other. The orientation of the first BAC end sequence must be "+"; that of the second BAC end sequence must be "-".
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 annotation can also be used to determine which BAC contains a given gene, useful information for certain wet lab experiments.
This track shows mappings in cases where both ends could be mapped. For the $organism assembly, the BACs are approximately 150-200 kb in size and are used for both the fingerprint contig (FPC) and radiation hybrid (RH) maps.
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).
This track follows the display conventions for PSL alignment tracks. On the track description page, the display may be configured to show only those items with an unnormalized score that equals or exceeds a user-specified minimum.
To view the registry entry for a specific clone, open the details page for the clone and click on its name at the top of the page. Not all $organism BAC clones have been submitted to NCBI Clone Registry as of November 2006; therefore, some of the clone links to NCBI may not yet be active. Information about the libraries may be found on the Sanger Institute Zebrafish Library Details page. Additional information about some of the clones, including how they can be obtained, may be found at the NCBI Clone Registry.
Information about STS markers associated with a BAC clone is displayed when available. Aliases include those for the BAC clone and those for associated STS markers. The BAC ends tracks may be searched using the clone name, the Sanger internal BAC clone name, the Sanger STS name or any of these aliases. The UniSTS ID(s) shown are those associated with the STS aliases for each Sanger STS name.
NOTE: The primer sequences shown may differ from those associated with the uniSTS IDs in UniSTS. In cases where more than one UniSTS ID exists, primer sequences may be the same as those in UniSTS for one of the UniSTS IDs. The value in the relationship field indicates the method used to find the STS markers associated with a particular BAC clone:
BAC end sequences were placed on the assembled sequence using blat, followed by pslReps using the parameters -nearTop=0.02 -minCover=0.40 -minAli=0.85 -noIntrons. This ensured that only alignments with least 85% identity, a minimum sequence coverage of 40% and a base identity level within 2% of the best were kept. No penalty was imposed for sequences that lacked introns. Furthermore, a base identity of at least 91% was required of at least one BAC end of the pair.
The $Organism BAC End Pairs track was produced at UCSC from data obtained from the following sources:
This track was produced in collaboration with the Zebrafish Genome Initiative at Childrens Hospital, Boston.
Kent, W.J. BLAT - the BLAST-like alignment tool. Genome Res. 12(4), 656-664 (2002).