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De novo search for non-coding RNA genes in the AT-rich genome of Dictyostelium discoideum : Performance of Markov-dependent genome feature scoring
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- Larsson, Pontus (författare)
- Uppsala universitet,Institutionen för cell- och molekylärbiologi
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- Hinas, Andrea (författare)
- Uppsala universitet,Institutionen för medicinsk biokemi och mikrobiologi
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- Ardell, David H. (författare)
- Uppsala universitet,Centrum för bioinformatik
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- Kirsebom, Leif A. (författare)
- Uppsala universitet,Institutionen för cell- och molekylärbiologi
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- Virtanen, Anders (författare)
- Uppsala universitet,Molekylärbiologi
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Söderbom, Fredrik (författare)
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(creator_code:org_t)
- 2008-03-17
- 2008
- Engelska.
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Ingår i: Genome Research. - : Cold Spring Harbor Laboratory. - 1088-9051 .- 1549-5469. ; 18:6, s. 888-899
- Relaterad länk:
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http://genome.cshlp....
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https://urn.kb.se/re...
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https://doi.org/10.1...
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Abstract
Ämnesord
Stäng
- Genome data are increasingly important in the computational identification of novel regulatory non-coding RNAs (ncRNAs). However, most ncRNA gene-finders are either specialized to well-characterized ncRNA gene families or require comparisons of closely related genomes. We developed a method for de novo screening for ncRNA genes with a nucleotide composition that stands out against the background genome based on a partial sum process. We compared the performance when assuming independent and first-order Markov-dependent nucleotides, respectively, and used Karlin-Altschul and Karlin-Dembo statistics to evaluate the significance of hits. We hypothesized that a first-order Markov-dependent process might have better power to detect ncRNA genes since nearest-neighbor models have been shown to be successful in predicting RNA structures. A model based on a first-order partial sum process (analyzing overlapping dinucleotides) had better sensitivity and specificity than a zeroth-order model when applied to the AT-rich genome of the amoeba Dictyostelium discoideum. In this genome, we detected 94% of previously known ncRNA genes (at this sensitivity, the false positive rate was estimated to be 25% in a simulated background). The predictions were further refined by clustering candidate genes according to sequence similarity and/or searching for an ncRNA-associated upstream element. We experimentally verified six out of 10 tested ncRNA gene predictions. We conclude that higher-order models, in combination with other information, are useful for identification of novel ncRNA gene families in single-genome analysis of D. discoideum. Our generalizable approach extends the range of genomic data that can be searched for novel ncRNA genes using well-grounded statistical methods.
Ämnesord
- NATURVETENSKAP -- Biologi -- Biokemi och molekylärbiologi (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Biochemistry and Molecular Biology (hsv//eng)
Nyckelord
- Cell and molecular biology
- Cell- och molekylärbiologi
Publikations- och innehållstyp
- ref (ämneskategori)
- art (ämneskategori)
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