Schema for BAC End Pairs - BAC End Pairs
  Database: dm3    Primary Table: bacEndPairs    Row Count: 11,938   Data last updated: 2006-08-18
Format description: Standard linked features series table
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 73smallint(6) range Bin number for browser speedup
chrom chr2Lvarchar(15) values Reference sequence chromosome or scaffold
chromStart 9394int(10) unsigned range Start position of clone in chromosome
chromEnd 175942int(10) unsigned range End position of clone in chromosome
name BACR09J20varchar(100) values Name of clone
score 1000int(10) unsigned range 1000 if uniquely aligned, else 1500/(# of alignments to assembly)
strand +char(2) values Value should be + or -
pslTable all_bacendsvarchar(50) values Table which contains corresponding PSL records for linked features
lfCount 2int(10) unsigned range Number of linked features in the series
lfStarts 9394,175167longblob   Comma separated list of start positions of each linked feature in genomic
lfSizes 796,775longblob   Comma separated list of sizes of each linked feature in genomic
lfNames AL0AA009DE10C1,AL0AA009DE10A1longblob   Comma separated list of names of linked features

Connected Tables and Joining Fields
        dm3.all_bacends.qName (via bacEndPairs.lfNames)

Sample Rows
 
binchromchromStartchromEndnamescorestrandpslTablelfCountlfStartslfSizeslfNames
73chr2L9394175942BACR09J201000+all_bacends29394,175167796,775AL0AA009DE10C1,AL0AA009DE10A1
73chr2L23735175934BACR31E171000+all_bacends223735,175000982,934AL0AA031AC09C1,AL0AA031AC09A1
585chr2L3164383344BACN08N121000-all_bacends231643,82538795,806AM0AA008DG06BP1,AM0AA008DG06CP1
73chr2L70020232786BACR11N221000-all_bacends270020,231890931,896AL0AA011DG11A1,AL0AA011DG11C1
73chr2L74302256667BACR17J091000+all_bacends274302,255786946,881AL0AA017CE05C2,AL0AA017CE05A2
73chr2L79768239466BACR35H071000+all_bacends279768,2384451015,1021AL0AA035CD04C1,AL0AA035CD04A1
73chr2L90195251537BACR37B151000-all_bacends290195,250581970,956AL0AA037CA08A1,AL0AA037CA08C1
73chr2L90199256669BACR03N131000-all_bacends290199,2555491049,1120AL0AA003CG07A1,AL0AA003CG07C1
73chr2L140231299445BACR05P011000+all_bacends2140231,298480907,965AL0AA005CH01C1,AL0AA005CH01A1
73chr2L142937347737BACR17J141000-all_bacends2142937,346745972,992AL0AA017DE07A2,AL0AA017DE07C2

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.

BAC End Pairs (bacEndPairs) Track Description
 

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 (https://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.