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 and can be accessed from BACPAC Genomics. This annotation can also be used to determine which BAC contains a given gene, useful information for certain wet lab experiments.
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).
Items are displayed as two blocks (one for each BAC end) connected by a thin line spanning the inferred BAC insert. Darker items indicate higher confidence alignments.
BAC end sequences were originally placed on the danRer4 (Zv6) assembly using BLAT, followed by pslReps with the parameters -nearTop=0.02 -minCover=0.40 -minAli=0.85 -noIntrons. This ensured that only alignments with at least 85% identity, a minimum sequence coverage of 40% and a base identity level within 2% of the best were kept. A base identity of at least 91% was required of at least one BAC end of the pair.
The danRer11 (GRCz11) coordinates were produced by lifting the danRer4 annotations using the UCSC liftOver tool. Of the original 154,632 BAC end pairs, 134,131 (87%) mapped successfully to danRer11.
The Zebrafish 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 WJ. BLAT--the BLAST-like alignment tool. Genome Res. 2002 Apr;12(4):656-64. PMID: 11932250; PMC: PMC187518