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Finding genes in DNA using decision trees and dynamic programming

S Salzberg, X Chen, J Henderson, K Fasman
1996 Proceedings. International Conference on Intelligent Systems for Molecular Biology  
The system uses a dynamic programming algorithm that finds the optimal segmentation of a DNA sequence into coding and non-coding regions (exons and introns).  ...  This study demonstrates the use of decision tree classifiers as the basis for a general gene-finding system.  ...  IRI-9116843 and IRI-9223591, and by a "t%ung Faculty Research Initiative grant from the G.W.C. Whiting School of Engineering at, Johns Hopkins University.  ... 
pmid:8877520 fatcat:t5l4b5tu7nazxn3ww3oak7hsoi

Gene Identification: Classical and Computational Intelligence Approaches

S. Bandyopadhyay, U. Maulik, D. Roy
2008 IEEE Transactions on Systems Man and Cybernetics Part C (Applications and Reviews)  
Compared to earlier attempts for finding genes, the recent techniques are significantly more accurate and reliable.  ...  In addition, a long list of available gene finders is compiled.  ...  ACKNOWLEDGMENT The authors gratefully acknowledge the informative comments of the reviewers that helped in improving the quality of the manuscript.  ... 
doi:10.1109/tsmcc.2007.906066 fatcat:g7idd6l4uzboxmm3yckleyz75e

A Decision Tree System for Finding Genes in DNA

STEVEN SALZBERG, ARTHUR L. DELCHER, KENNETH H. FASMAN, JOHN HENDERSON
1998 Journal of Computational Biology  
The decision tree system is combined with new methods for identifying start codons, donor sites, and acceptor sites, and these are brought together in a frame-sensitive dynamic programming algorithm that  ...  MORGAN is an integrated system for nding genes in vertebrate DNA sequences.  ...  K01-HG00022-1 and by the National Science foundation under Grant Nos. IRI-9223591 and IRI-9530462. KHF is supported by the Department of Energy under award number DE-  ... 
doi:10.1089/cmb.1998.5.667 pmid:10072083 fatcat:kjavi7c6jzhhjnkxyy5xzoys2q

GlimmerM, Exonomy and Unveil: three ab initio eukaryotic genefinders

W. H. Majoros
2003 Nucleic Acids Research  
We present three programs for ab initio gene prediction in eukaryotes: Exonomy, Unveil and GlimmerM.  ...  Exonomy is a 23-state Generalized Hidden Markov Model (GHMM), Unveil is a 283-state standard Hidden Markov Model (HMM) and GlimmerM is a previously-described genefinder which utilizes decision trees and  ...  ACKNOWLEDGEMENTS This work was supported in part by NSF grants MCB-0114792 and KDI-9980088, and by NIH grant R01-LM06845.  ... 
doi:10.1093/nar/gkg527 pmid:12824375 pmcid:PMC168934 fatcat:f56fqvuyjbccbecu6dw642yara

CBSTD: A Cloud Based Symbol Table Driven DNA Compression Algorithm [chapter]

Annwesha Banerjee Majumder, Somsubhra Gupta
2017 Lecture Notes in Networks and Systems  
Different symbols for the different sequence of occurrence of DNA sequence has been chosen and compressed the sequence. Dynamic programming concepts have been explored in the proposed algorithm.  ...  In this paper, a DNA sequence compression algorithm through substitution mechanism has been proposed.  ...  Dynamic programming technique can also be used to compress DNA sequence and that was proposed by Behshad Behzadi et al.  ... 
doi:10.1007/978-981-10-3953-9_45 fatcat:cbz32e5vybcrpdybvdp3hlcydu

Constraint-Based System for Genomic Analysis

Nittaya Kerdprasop, Kittisak Kerdprasop
2015 International Journal of Information and Education Technology  
In this paper, we propose a different setting of sequence analysis formulation based on the nucleotide patterns using a constraint logic programming paradigm, in which the sequence alignment can be performed  ...  His current research includes data mining, artificial intelligence, functional and logic programming languages, computational statistics.  ...  ACKNOWLEDGMENT This work has been supported by grants from the National Research Council of Thailand (NRCT) and the authors are supported by research funding from Suranaree University of Technology.  ... 
doi:10.7763/ijiet.2015.v5.487 fatcat:jxutnxbhvjedlfn22ksfntkz2m

Computational methods for the identification of genes in vertebrate genomic sequences

J. Claverie
1997 Human Molecular Genetics  
Research into new methods to identify genes in anonymous genomic sequences has been going on for more than 15 years.  ...  The best program currently available perfectly locates more than 80% of the internal coding exons, and only 5% of the predictions do not overlap a real exon.  ...  Decision tree MORGAN (60), an integrated system for finding genes, uses a variety of techniques, the most distinctive of which is a 'decision tree' algorithm.  ... 
doi:10.1093/hmg/6.10.1735 pmid:9300666 fatcat:qwjro6ogvnftfd4g67kskvxxie

Computational Gene Prediction Using Multiple Sources of Evidence

J. E. Allen
2003 Genome Research  
The program, called Combiner, takes as input a genomic sequence and the locations of gene predictions from ab initio gene finders, protein sequence alignments, expressed sequence tag and cDNA alignments  ...  Our results show that combining gene prediction evidence consistently outperforms even the best individual gene finder and, in some cases, can produce dramatic improvements in sensitivity and specificity  ...  To address these limitations, we developed a statistical scoring method that uses decision trees (in particular, the randomized oblique decision trees of Murthy et al. 1994 ) to correlate evidence patterns  ... 
doi:10.1101/gr.1562804 pmid:14707176 pmcid:PMC314291 fatcat:u3sgyq4yejh7nikz5jsxtnbn7e

Improving the performance of Transposable Elements detection tools

Tiago Loureiro, Rui Camacho, Jorge Vieira, Nuno A. Fonseca
2013 Journal of Integrative Bioinformatics  
SummaryTransposable Elements (TE) are sequences of DNA that move and transpose within a genome.  ...  In this paper we evaluate the performance of several TEs detection and annotation tools and investigate if Machine Learning techniques can be used to improve their overall detection accuracy.  ...  This work was financed by the ERDF -European Regional Development Fund through the COMPETE Program (operational program for competitiveness) and by National Funds through the FCT -Fundac ¸ão para a Ciência  ... 
doi:10.1515/jib-2013-231 fatcat:bdcykft5fbcetlkthf7u4ymzha

JIGSAW: integration of multiple sources of evidence for gene prediction

J. E. Allen, S. L. Salzberg
2005 Bioinformatics  
JIGSAW computes the relative weight of different lines of evidence using statistics generated from a training set, and then combines the evidence using dynamic programming.  ...  Motivation: Computational gene finding systems play an important role in finding new human genes, although no systems are yet accurate enough to predict all or even most protein-coding regions perfectly  ...  Majoros and Mihaela Pertea for extraction of RefSeq genes and for numerous useful comments and suggestions.  ... 
doi:10.1093/bioinformatics/bti609 pmid:16076884 fatcat:25nai6xrwzdetp25dwhdxxa4ha

Improving the performance of Transposable Elements detection tools

Tiago Loureiro, Rui Camacho, Jorge Vieira, Nuno A Fonseca
2013 Journal of Integrative Bioinformatics  
Transposable Elements (TE) are sequences of DNA that move and transpose within a genome.  ...  In this paper we evaluate the performance of several TEs detection and annotation tools and investigate if Machine Learning techniques can be used to improve their overall detection accuracy.  ...  This work was financed by the ERDF -European Regional Development Fund through the COMPETE Program (operational program for competitiveness) and by National Funds through the FCT -Fundação para a Ciência  ... 
doi:10.2390/biecoll-jib-2013-231 pmid:24231145 fatcat:szraidwb35eypbig6fj6cxht5u

Sequence Relationships Similarity Of Swine Influenza A (H1N1) Virus

Patsaraporn Somboonsak, Mud-Armeen Munlin
2011 Zenodo  
Nucleic acid sequence Maximum Likelihood (MCL) and DNA Empirical base frequencies, Phylogenetic relationship amongst the HA genes of H1N1 virus isolated in Genbank having high nucleotide sequence homology  ...  In this paper we used 16 HA nucleotide sequences from NCBI for computing sequence relationships similarity of swine influenza A virus using the following method MCL the result is 28%, 36.64% for Optimal  ...  The methods most frequently used for DNA analyses and prediction region are based on machine learning methods, such as neural networks, decision trees and others. II.  ... 
doi:10.5281/zenodo.1056453 fatcat:si7odpipavedhhudmpcvw77svq

The Utilization Of Genetic Approaches For Effective Conservation Of Endangered Species Congress Project, Regional Workshop, Zvolen, January 25– 27, 2012

Małgorzata Sułkowska
2012 Zenodo  
-Where could be find funding to build on their achievements in genetic decision-making processes regarding environmental protection?  ...  of organisms, population genetic structure dynamics e.g. selection, gene flow methods of elaboration and many, many other problems.  ... 
doi:10.5281/zenodo.30874 fatcat:2e3k6gb7jnafvf2qqwdmynk6eq

Page 3483 of Mathematical Reviews Vol. , Issue 2004d [page]

2004 Mathematical Reviews  
Though the default alphabet for the program is the DNA alphabet {A,G,C,T}, it is designed to accept (or generate) words over an arbitrary alphabet and as such it can be used for a variety of applications  ...  Summary: “In DNA nanotechnology and DNA based computa- tions the design of DNA sequences that are error resistant is of essential importance.  ... 

Robust dynamic balance of AP-1 transcription factors in a neuronal gene regulatory network

Gregory M Miller, Babatunde A Ogunnaike, James S Schwaber, Rajanikanth Vadigepalli
2010 BMC Systems Biology  
We investigated the robustness of this behavior to simultaneous perturbations in the network parameters using a novel multivariate approach that integrates global sensitivity analysis with decision-tree  ...  This modulation occurs via activation of a complex network of signaling proteins and transcription factors, leading to changes in levels of key genes and proteins.  ...  RV supervised the study, formulated the mathematical model, designed the combination of sensitivity and decision-tree analysis methods, assisted in interpretation and presentation of the results, and drafted  ... 
doi:10.1186/1752-0509-4-171 pmid:21167049 pmcid:PMC3019179 fatcat:lymq5ienpfajxbrrg6lqnuymrq
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