Sequencing libraries
Libraries utilised in this project
Essentially two types of plasmid library are constructed in the project:
Chromosomal libraries
DNA material is directly purified from pulsed-field gels and then cloned into pUC18. More than one library may have been constructed for each chromosome, identified by a unique ligation identifier. All chromosomal libraries are named after the chromosome they were constructed from and can be browsed here.
Potential contaminants of these libraries are sequencing vector (pUC18) and E.coli. The most pertenant thing to remember about these libraries are that they are chromosomally enriched, and not chromosomally pure. Therefore something in the order of 15-20 % of the library will originate from a different chromosome. We make every effort to identify such reads and are presently working on formalising screening procedures to 'bin' such reads into chromosome-specific databases.
The genome is being sequenced via a cosmid clone methodology with a chromosomal skim. These pages are designed to explain the naming schema for these libraries which will allow you to identify where any shotgun read was produced, and identify potential problems associated with the data.
P1 clone libraries
Clone inserts are purified from preparatory agarose gels and then cloned into pUC18. All libraries are named after the clone they were constructed from and can be browsed here. All clones originate from the TREU 927/4 strain.
We make every effort to identify such reads but know that many exist within the database. We are presently working on a more efficient screening procedure.
Shotgun read naming nomenclature
All shotgun reads are given a unique name which includes information about:
- Starting DNA material from which the library was constructed
- Plate position
- Strand sequenced
- Primer used in sequencing
- Conditions used in sequencing
- Repitition of the sequencing read
P1 clone libraries
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Chromosomal Shotgun read libraries
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