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Bioinformatics Advance Access originally published online on December 7, 2004
Bioinformatics 2005 21(8):1695-1698; doi:10.1093/bioinformatics/bti181
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© The Author 2004. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oupjournals.org

TERMINUS—Telomeric End-Read Mining IN Unassembled Sequences

Weixi Li 1, Cathryn J. Rehmeyer 2, Chuck Staben 1 and Mark L Farman 2,*

1Department of Biological Sciences, University of Kentucky Lexington, KY 40546, USA
2Department of Plant Pathology, University of Kentucky Lexington, KY 40546, USA

*To whom correspondence should be addressed.

Summary: TERMINUS is a set of tools to map telomeres on draft sequences of whole genome shotgun sequencing projects. It mines raw sequence reads (from a trace archive) for telomeric reads, assembles them into contigs representing individual chromosome ends and BLASTs the resulting consensus sequences against the genome assembly to identify telomere-proximal genomic contigs. Finally, it estimates the sizes of telomeric gaps and identifies clones for gap closure. TERMINUS is implemented as a set of Perl scripts that requires two sets of inputs: the NCBI Trace Archive files for a given genome project; and ancillary genome assembly information. Results are output in spreadsheets containing information that facilitates manual validation.

Availability: The TERMINUS package and supplementary information can be downloaded from http://www.genome.kbrin.uky.edu/fungi_tel/terminus/

Contact: farman{at}uky.edu


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