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Dfam: a database of repetitive DNA based on profile hidden Markov models
- Source :
- Nucleic Acids Research
- Publication Year :
- 2012
- Publisher :
- Oxford University Press (OUP), 2012.
-
Abstract
- We present a database of repetitive DNA elements, called Dfam (http://dfam.janelia.org). Many genomes contain a large fraction of repetitive DNA, much of which is made up of remnants of transposable elements (TEs). Accurate annotation of TEs enables research into their biology and can shed light on the evolutionary processes that shape genomes. Identification and masking of TEs can also greatly simplify many downstream genome annotation and sequence analysis tasks. The commonly used TE annotation tools RepeatMasker and Censor depend on sequence homology search tools such as cross_match and BLAST variants, as well as Repbase, a collection of known TE families each represented by a single consensus sequence. Dfam contains entries corresponding to all Repbase TE entries for which instances have been found in the human genome. Each Dfam entry is represented by a profile hidden Markov model, built from alignments generated using RepeatMasker and Repbase. When used in conjunction with the hidden Markov model search tool nhmmer, Dfam produces a 2.9% increase in coverage over consensus sequence search methods on a large human benchmark, while maintaining low false discovery rates, and coverage of the full human genome is 54.5%. The website provides a collection of tools and data views to support improved TE curation and annotation efforts. Dfam is also available for download in flat file format or in the form of MySQL table dumps.
- Subjects :
- Flat file database
Biology
computer.software_genre
Genome
03 medical and health sciences
Annotation
0302 clinical medicine
Genetics
Humans
Hidden Markov model
030304 developmental biology
Internet
0303 health sciences
Models, Statistical
Markov chain
Database
Genome, Human
Molecular Sequence Annotation
Articles
Genome project
Markov Chains
DNA Transposable Elements
Human genome
Databases, Nucleic Acid
computer
030217 neurology & neurosurgery
Subjects
Details
- ISSN :
- 13624962 and 03051048
- Volume :
- 41
- Database :
- OpenAIRE
- Journal :
- Nucleic Acids Research
- Accession number :
- edsair.doi.dedup.....19fbaca8d01822db45fa7beaaedb9e15