Guide To Working With Repeated Elements

Question

[Eric Fournier]

Would anyone happen to know a good guide/review article/book about working with Repeated elements in bioinformatics? Personally, my knowledge of repeats come from bits and pieces I've put together from Wikipedia, my biology textbooks and the RepeatMasker manual. I've yet to find a single comprehensive ressource I can use as a "go to" reference for colleagues that are new to the subject.

Reviews about repeated elements at large could also be useful.

Answer 1

[Casey Bergman]

A trio of reviews on transposable element bioinformatics came out from 2007-2010 that cover this area fairly well:

• Discovering and detecting transposable elements in genome sequences. http://www.ncbi.nlm.nih.gov/pubmed/17932080
• Computational Approaches and Tools Used in Identification of Dispersed Repetitive DNA Sequences http://www.springerlink.com/content/w25780161625k718/
• Identifying repeats and transposable elements in sequenced genomes: how to find your way through the dense forest of programs. http://www.ncbi.nlm.nih.gov/pubmed/19935826

See also a page on TE bioinformatics tools I maintain here: http://bergmanlab.smith.man.ac.uk/?page_id=295

[Larry_Parnell]

Thanks, Casey. This is the kind of info that would be exceedingly difficult to find with contacting an expert and shows why BioStar is indeed a great resource. I intend to save these references myself.

[Eric Fournier]

Very useful! Thanks a lot.

[David M]

I'm beginning an annotation project and these are great resources. Thanks!