Projector 2 -- contig mapping for efficient gap-closure of prokaryotic genome sequence assemblies
What you can do:
Automatically position contigs from an unfinished prokaryotic genome onto (parts of) a template genome of a closely related strain or species in order to close a significant number of remaining gaps in the late stages of a genome sequencing project.
Highlights:
- Projector 2 uses (un)finished genomic sequences of an organism as a template to infer linkage information for a genome sequence assembly of a related organism being sequenced.
- The remaining gaps between contigs for which no linkage information is present can subsequently be closed with direct PCR strategies.
- Compared with other implementations, Projector 2 has several distinctive features: a user-friendly web interface, automatic removal of repetitive elements (repeat-masking) and automated primer design for gap-closure purposes.
- Moreover, when using multiple fragments of a template genome, primers for multiplex PCR strategies can also be designed. Primer design takes into account that, in many cases, contig ends contain unreliable DNA sequences and repetitive sequences.
- Closing the remaining gaps in prokaryotic genome sequence assemblies is thereby made very efficient and virtually effortless.
Keywords:
- prokaryotic genomes
- prokaryotic genome sequence assembly tool
- PCR primers
- PCR primer design tool
- multiplex PCR primers
- multiplex PCR primer design tool
- contig mapping tool
- bacterial genomes
Literature & Tutorials:
This record last updated: 12-19-2005