Clones and Libraries
Integration of clone-based information requires that data producers use a consistent scheme for naming clones. For this purpose, the Clone Registry uses a database- assigned library identifier together with plate/row/column address.
BAC End Sequencing
High-throughput end sequencing of BAC clones has become a popular way to simultaneously characterize libraries and survey genomes. These sequences have been called 'sequence tagged connectors' (STCs) by Mahairas, et al., who have demostrated utility in seeding the sequencing process and building clone based maps. More recently, BAC ends have been incorporated as adiitional paired reads into whole genome shotgun (WGS) assemblies in order to provide more long-range continuity.
Clone Registration
To avoid unnecessary duplication of effort, genomic sequencing groups can register their intent to sequence specific clones and advise the database of changes in their sequencing status. In addition, automated monitoring of daily GenBank submissions provides direct links between clones and their accession numbers.
BACs as FISH Reagents
The Human BAC Resource provides a genome-wide collection of clones that have been used as fluorescent in situ hybridization (FISH) probes for integrating cytogenetic, radiation-hybrid, linkage and sequence maps of the human genome. Some of these clones have been mapped at very high-resolution as part of the NIH Cancer Chromosome Abberations Project (CCAP).
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Displaying Clones in Map Viewer
BAC-end sequences are used in the NCBI Genome Annotation pipeline to pinpoint the genomic locations of many clones (although some cannot be placed if the sequences are too repititive). Use the search form below to find clones and view in the context of other features, such as genes. For additional details and more search options, refer to the Map Viewer page for the organism of interest.
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Finding Clones Near a Genomic Feature
A common task is to identify a BAC clone that contains some specific feature such as a gene or a marker. Although this can be done by inspection using MapViewer, the Clone Finder facility allows it to be done by direct querying (however, it is currently available only for mouse). Use the form below to search for clones near a given mouse gene. For more options, see the Clone Finder home page.
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BLAST BAC end sequences
BAC end sequences are stored in the genome survey sequence (GSS) division of GenBank and made available for BLAST searching. For convenience, the form below provides organism-specific subsets of BAC end sequences for searching.
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NCBI
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Clone Nomenclature
Mahairas, et al. (1999)
