TERMINUS - Telomeric end-read mining IN unassembled sequences

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

doi:10.1093/bioinformatics/bti181

TERMINUS - Telomeric end-read mining IN unassembled sequences

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

Research output: Contribution to journal › Article › peer-review

18 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 language	English
Pages (from-to)	1695-1698
Number of pages	4
Journal	Bioinformatics
Volume	21
Issue number	8
DOIs	https://doi.org/10.1093/bioinformatics/bti181
State	Published - 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.

Funding

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.

Funders	Funder number
Kentucky Biomedical Research Infrastructure Network Bioinformatics Core	5P20RR016481-03
National Science Foundation (NSF)	MCB-0135462
National Center for Research Resources	P20RR016481
University of Louisville

ASJC Scopus subject areas

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

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10.1093/bioinformatics/bti181

Cite this

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title = "TERMINUS - Telomeric end-read mining IN unassembled sequences",

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.",

author = "Weixi Li and Rehmeyer, \{Cathryn J.\} and Chuck Staben and Farman, \{Mark L.\}",

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.",

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doi = "10.1093/bioinformatics/bti181",

language = "English",

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AU - Li, Weixi

AU - Rehmeyer, Cathryn J.

AU - Staben, Chuck

AU - Farman, Mark L.

N1 - 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.

PY - 2005/4/15

Y1 - 2005/4/15

N2 - 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.

AB - 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.

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JO - Bioinformatics

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IS - 8

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TERMINUS - Telomeric end-read mining IN unassembled sequences

Abstract

Bibliographical note

Funding

ASJC Scopus subject areas

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