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TERMINUS--Telomeric End-Read Mining IN Unassembled Sequences.

Weixi Li·Cathryn J Rehmeyer·Chuck Staben·Mark L Farman
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Abstract

UNLABELLED: 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@uky.edu.

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AlgorithmsChromosome MappingDatabase Management SystemsDatabases, GeneticInformation Storage and RetrievalSequence Analysis, DNASoftwareTelomereUser-Computer InterfaceJournal ArticleResearch Support, N.I.H., ExtramuralResearch Support, U.S. Gov't, Non-P.H.S.Research Support, U.S. Gov't, P.H.S.

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Weixi Li, Cathryn J Rehmeyer, Chuck Staben, Mark L Farman. 2004-12-07. TERMINUS--Telomeric End-Read Mining IN Unassembled Sequences.. https://doi.org/10.1093/bioinformatics%2Fbti181

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