Bacterial artificial chromosomes (BACs) are a key part of many large scale sequencing projects and for $organism, they were used for both the FPC and the RH maps. A BAC typically consists of 50 - 300 kb of DNA. For $organism, the BAC clones are in the range of 2 - 650 kb with the average size being approximately 170 kb. 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.
A valid pair of BAC end sequences must be at least 2 kb but no more than 800 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 "-". There are replicate reads for some BAC end sequences - these have similar read names and the BAC clone name is the same in each case. If reads for the same BAC clone have identical alignments, they are shown on the same description page.
The scoring scheme used allocates 1000 to an alignment when the BAC end pairs only aligned to one location in the genome (after filtering). For multiple alignments to the genome, a BAC end pair or clone scores 1500/Number of alignments.
BAC end sequences are placed on the assembled sequence using Jim Kent's blat program followed by pslReps using parameters such 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 and there was no penalty for not having introns (-nearTop=0.02 -minCover=0.40 -minAli=0.85 -noIntrons). Furthermore, a base identity of at least 91% was required of at least one BAC end of the pair.
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. 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 July 2004; therefore, some of the clone links to NCBI may not yet be active.
The $Organism BAC End Pairs track was produced at UCSC from BAC End Pairs sequence data obtained from Robert Geisler at the Max Planck Institute for Developmental Biology, Germany and the Netherlands Institute for Developmental Biology (Hubrecht Laboratory). The track was produced in collaboration with the Zebrafish Genome Initiative at Childrens Hospital, Boston. GenBank accessions for BAC clones were obtained from The Wellcome Trust Sanger Institute, Cambridge, United Kingdom.