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Bioinformatics Advance Access published online on December 7, 2004
Bioinformatics, doi:10.1093/bioinformatics/bti181
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Bioinformatics © Oxford University Press 2004; all rights reserved.
Received March 14, 2004
Revised November 8, 2004
Accepted November 23, 2004

Applications note

TERMINUS - telomeric end-read mining IN unassembled sequences

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

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

* To whom correspondence should be addressed.
Mark L. Farman, E-mail: farman{at}uky.edu


  Abstract

Summary: TERMINUS is a set of tools to map telomeres on draft sequences of whole genome shotgun sequencing projects. It mines raw sequence reads (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://genome.kbrin.uky.edu/fungi_tel/terminus/.


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