TERMINUS - Telomeric end-read mining IN unassembled sequences

Weixi Li, Cathryn J. Rehmeyer, Chuck Staben, Mark L. Farman

Research output: Contribution to journalArticlepeer-review

17 Scopus citations

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 (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.

Original languageEnglish
Pages (from-to)1695-1698
Number of pages4
JournalBioinformatics
Volume21
Issue number8
DOIs
StatePublished - Apr 15 2005

Bibliographical note

Funding Information:
This work was supported by a subcontract to Chuck Staben from the Kentucky Biomedical Research Infrastructure Network, 5P20RR016481-03, awarded to Nigel Cooper of the University of Louisville, by the National Center for Research Resources and by a National Science Foundation award, MCB-0135462, to Mark Farman. This is Kentucky Agricultural Experiment Station publication 04-12-186.

ASJC Scopus subject areas

  • Statistics and Probability
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Computational Theory and Mathematics
  • Computational Mathematics

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