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 | |
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