| Literature DB >> 19936833 |
Andrey Shirak1, Manfred Grabherr, Federica Di Palma, Kerstin Lindblad-Toh, Gideon Hulata, Micha Ron, Tom D Kocher, Eyal Seroussi.
Abstract
The large-scale bacterial artificial chromosome-end sequencing project of Nile tilapia (Oreochromis niloticus) has generated extensive sequence data that allowed the examination of the repeat content in this fish genome and building of a repeat library specific for this species. This library was established based on Tilapiini repeat sequences from GenBank, sequences orthologous to the repeat library of zebrafish in Repbase, and novel repeats detected by genome analysis using MIRA assembler. We estimate that repeats constitute about 14% of the tilapia genome and also give estimates for the occurrence of the different repeats based on the Basic Local Alignment Search Tool searches within the database of known tilapia sequences. The frequent occurrence of novel repeats in the tilapia genome indicates the importance of using the species-specific repeat masker prior to sequence analyses. A web tool based on the RepeatMasker software was designed to assist tilapia genomics.Entities:
Mesh：
Year: 2009 PMID： 19936833 PMCID： PMC3178446 DOI： 10.1007/s10126-009-9236-8
Source DB: PubMed Journal: Mar Biotechnol (NY) ISSN： 1436-2228 Impact factor: 3.619