A new method to compute K-mer frequencies and its application to annotate large repetitive plant genomes

• Published in: BMC genomics Vol. 9; no. 1; p. 517
• Main Authors: Kurtz, Stefan, Narechania, Apurva, Stein, Joshua C, Ware, Doreen
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 31.10.2008; BioMed Central; BMC
• Subjects: Applications software; Computational biology; Computational Biology - methods; DNA Transposable Elements; Genome, Plant; Genomics - methods; Methodology; Methods; Oryza; Physiological aspects; Plant genetics; Software; Sorghum; Transposons; Zea mays; Germany

The challenges of accurate gene prediction and enumeration are further aggravated in large genomes that contain highly repetitive transposable elements (TEs). Yet TEs play a substantial role in genome evolution and are themselves an important subject of study. Repeat annotation, based on counting oc...