TERMINUS—Telomeric End-Read Mining IN Unassembled Sequences

• Published in: Bioinformatics 2005-04, Vol.21 (8), p.1695-1698
• Main Authors: Li, Weixi, Rehmeyer, Cathryn J., Staben, Chuck, Farman, Mark L
• Format: Article
• Language: English
• Subjects: Algorithms; Biological and medical sciences; Chromosome Mapping - methods; Database Management Systems; Databases, Genetic; Fundamental and applied biological sciences. Psychology; General aspects; Information Storage and Retrieval - methods; Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects); Sequence Analysis, DNA - methods; Software; Telomere - genetics; User-Computer Interface
• ISSN: 1367-4803; 1460-2059; 1367-4811
• DOI: 10.1093/bioinformatics/bti181

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: [e-mail]