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A branch point consensus from Arabidopsis found by non-circular analysis allows for better prediction of acceptor sites

(1997) NUCLEIC ACIDS RESEARCH. 25(15). p.3159-3163
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Abstract
Little knowledge exists about branch points in plants; it has even been claimed that plant introns lack conserved branch point sequences similar to those found in vertebrate introns. A putative branch point consensus sequence for Arabidopsis thaliana resembling the well known metazoan consensus sequence has been proposed, but this is based on search of sequences similar to those in yeast and metazoa. Here we present a novel consensus sequence found by a non-circular approach. A hidden Markov model with a fixed A nucleotide was trained on sequences upstream of the acceptor site. The consensus found by the Markov model shares features with the metazoan consensus, but differs in its details from the consensus proposed earlier. Despite the fact that branch point consensus sequences in plants are weak, we show that a prediction scheme incorporating them leads to a substantial improvement in the recognition of true acceptor sites; the false positive rate being reduced by a factor of 2. We take this as an indication that the consensus found here is the genuine one and that the branch point does play a role in the proper recognition of the acceptor site in plants.
Keywords
PROTEIN, SELECTION, INTRONS, SEQUENCES, 3' SPLICE-SITE

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Chicago
Tolstrup, Niels, Pierre Rouzé, and Søren Brunak. 1997. “A Branch Point Consensus from Arabidopsis Found by Non-circular Analysis Allows for Better Prediction of Acceptor Sites.” Nucleic Acids Research 25 (15): 3159–3163.
APA
Tolstrup, N., Rouzé, P., & Brunak, S. (1997). A branch point consensus from Arabidopsis found by non-circular analysis allows for better prediction of acceptor sites. NUCLEIC ACIDS RESEARCH, 25(15), 3159–3163.
Vancouver
1.
Tolstrup N, Rouzé P, Brunak S. A branch point consensus from Arabidopsis found by non-circular analysis allows for better prediction of acceptor sites. NUCLEIC ACIDS RESEARCH. 1997;25(15):3159–63.
MLA
Tolstrup, Niels, Pierre Rouzé, and Søren Brunak. “A Branch Point Consensus from Arabidopsis Found by Non-circular Analysis Allows for Better Prediction of Acceptor Sites.” NUCLEIC ACIDS RESEARCH 25.15 (1997): 3159–3163. Print.
@article{184569,
  abstract     = {Little knowledge exists about branch points in plants; it has even been claimed that plant introns lack conserved branch point sequences similar to those found in vertebrate introns. A putative branch point consensus sequence for Arabidopsis thaliana resembling the well known metazoan consensus sequence has been proposed, but this is based on search of sequences similar to those in yeast and metazoa. Here we present a novel consensus sequence found by a non-circular approach. A hidden Markov model with a fixed A nucleotide was trained on sequences upstream of the acceptor site. The consensus found by the Markov model shares features with the metazoan consensus, but differs in its details from the consensus proposed earlier. Despite the fact that branch point consensus sequences in plants are weak, we show that a prediction scheme incorporating them leads to a substantial improvement in the recognition of true acceptor sites; the false positive rate being reduced by a factor of 2. We take this as an indication that the consensus found here is the genuine one and that the branch point does play a role in the proper recognition of the acceptor site in plants.},
  author       = {Tolstrup, Niels and Rouz{\'e}, Pierre and Brunak, S{\o}ren},
  issn         = {0305-1048},
  journal      = {NUCLEIC ACIDS RESEARCH},
  keyword      = {PROTEIN,SELECTION,INTRONS,SEQUENCES,3' SPLICE-SITE},
  language     = {eng},
  number       = {15},
  pages        = {3159--3163},
  title        = {A branch point consensus from Arabidopsis found by non-circular analysis allows for better prediction of acceptor sites},
  url          = {http://dx.doi.org/10.1093/nar/25.15.3159},
  volume       = {25},
  year         = {1997},
}

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