PMID- 22099702
OWN - NLM
STAT- MEDLINE
DCOM- 20120702
LR  - 20111221
IS  - 1879-0534 (Electronic)
IS  - 0010-4825 (Linking)
VI  - 42
IP  - 1
DP  - 2012 Jan
TI  - Intron identification approaches based on weighted features and fuzzy decision 
      trees.
PG  - 112-22
LID - 10.1016/j.compbiomed.2011.10.015 [doi]
AB  - Current computational predictions of splice sites largely depend on the sequence 
      patterns of known intronic sequence features (ISFs) described in the classical 
      intron definition model (IDM). The computation-oriented IDM (CO-IDM) clearly 
      provides more specific and concrete information for describing intron flanks of 
      splice sites (IFSSs). In the paper, we proposed a novel approach of fuzzy 
      decision trees (FDTs) which utilize (1) weighted ISFs of twelve uni-frame 
      patterns (UFPs) and forty-five multi-frame patterns (MFPs) and (2) gain ratios to 
      improve the performances in identifying an intron. First, we fuzzified extracted 
      features from genomic sequences using membership functions with an unsupervised 
      self-organizing map (SOM) technique. Then, we brought in different viewpoints of 
      globally weighting and crossly referring in generating fuzzy rules, which are 
      interpretable and useful for biologists to verify whether a sequence is an intron 
      or not. Finally, the experimental results revealed the effectiveness of the 
      proposed method in improving the identification accuracy. Besides, we also 
      implemented an on-line intronic identifier to infer an unknown genomic sequence.
CI  - Copyright (c) 2011 Elsevier Ltd. All rights reserved.
FAU - Huang, Yin-Fu
AU  - Huang YF
AD  - Department of Computer Science and Information Engineering, National Yunlin 
      University of Science and Technology, 123 University Road Section 3, Touliu, 
      Yunlin, Taiwan 640, ROC. huangyf@yuntech.edu.tw
FAU - Liang, Ching-Ping
AU  - Liang CP
FAU - Liou, Sing-Wu
AU  - Liou SW
LA  - eng
PT  - Journal Article
DEP - 20111120
PL  - United States
TA  - Comput Biol Med
JT  - Computers in biology and medicine
JID - 1250250
SB  - IM
MH  - Computational Biology
MH  - *Decision Trees
MH  - *Fuzzy Logic
MH  - Humans
MH  - *Introns
MH  - *Models, Genetic
EDAT- 2011/11/22 06:00
MHDA- 2012/07/03 06:00
CRDT- 2011/11/22 06:00
PHST- 2010/08/25 00:00 [received]
PHST- 2011/04/11 00:00 [revised]
PHST- 2011/10/13 00:00 [accepted]
PHST- 2011/11/22 06:00 [entrez]
PHST- 2011/11/22 06:00 [pubmed]
PHST- 2012/07/03 06:00 [medline]
AID - S0010-4825(11)00211-3 [pii]
AID - 10.1016/j.compbiomed.2011.10.015 [doi]
PST - ppublish
SO  - Comput Biol Med. 2012 Jan;42(1):112-22. doi: 10.1016/j.compbiomed.2011.10.015. 
      Epub 2011 Nov 20.