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Gene recognition by combination of several gene-finding programs

K. Murakami, T. Takagi
1998 Bioinformatics  
Results: We have explored the effectiveness when the results of several gene-finding programs were re-analyzed and combined. We studied several methods with four programs (FEXH, GeneParser3,.  ...  By HIGHEST-policy combination method or BOUNDARY method, approximate correlation (AC) improved by 3-5% in comparison with the best single gene-finding program.  ...  Acknowledgement This work is partially supported by a Grant-in-Aid for Scientific Research on Priority Areas, 'Genome informatics' from the Ministry of Education, Science, Sports and Culture, Japan.  ... 
doi:10.1093/bioinformatics/14.8.665 pmid:9789092 fatcat:p5e2b2k7jzcqhg5eur3t4nqqk4

Gene Recognition Using Multiple Gene-Finding Programs

Katsuhiko Murakami, Toshihisa Takagi
1997 Genome Informatics Series  
This paper demonstrates how effective re-analysis of the results of multiple gene finding programs is. Four simple algorithms to integrate the results of some programs are proposed and tested.  ...  Our experiments show that it is effective to use multiple gene finding programs simultaneously. We also developed a client program by which one can easily use the algorithm through the Internet.  ...  Acknowledgments This work is partially supported by Grant-in-Aid for Scientific Research on Priority Areas, "Genome Science" from the Ministry of Education, Science, Sports and Culture, Japan.  ... 
doi:10.11234/gi1990.8.308 fatcat:nuun4dzfjrhevnnvj6lzgizd24

The Gene-Finder computer tools for analysis of human and model organisms genome sequences

V Solovyev, A Salamov
1997 Proceedings. International Conference on Intelligent Systems for Molecular Biology  
We have developed FEXHB and FGENEHB programs combining pattern recognition features and information about similarity of predicted exons with known sequences in protein databases.  ...  We present a complex of new programs for promoter, 3'-processing, splice sites, coding exons and gene structure identification in genomic DNA of several model species.  ...  They created artificial sequence by combining three one-gene GenBank entries (HUMCYPBE of 9 exons; HUMRASH of exons and HUMACTGA of 5 exons). Our program found exactly 3 genes in this sequence.  ... 
pmid:9322052 fatcat:u53iivjfjbe4jms4elpurelwdi

Computer model for recognition of functional transcription start sites in RNA polymerase II promoters of vertebrates

Vladimir B. Bajic, Seng Hong Seah, Allen Chong, S.P.T. Krishnan, Judice L.Y. Koh, Vladimir Brusic
2003 Journal of Molecular Graphics and Modelling  
It can be used in the context of gene finding through its recognition of the 5 end of genes.  ...  The system was evaluated on a large and diverse human sequence-set and exhibited several times higher accuracy than several publicly available TSS-finding programs.  ...  We compared the performance of our system to several other promoter recognition programs on the evaluation set.  ... 
doi:10.1016/s1093-3263(02)00179-1 pmid:12543131 fatcat:dwnwkxfl6vfanhseslcomy3v6a

An intelligent system for vertebrate promoter recognition

V.B. Bajic, A. Chong, Seng Hong Seah, V. Brusic
2002 IEEE Intelligent Systems  
PromoterInspector is a program with a considerably improved #TP/#FP ratio compared to several other promoter recognition programs. 3 Although PromoterInspector is a general promoter finding program,  ...  General gene recognition programs are trained to recognize broad classes of genes.  ...  His research interests include software engineering and programming in bioinformatics. He holds a BS in computer science from Nanyang Technological University, Singapore.  ... 
doi:10.1109/mis.2002.1024754 fatcat:xgm4f3kwdffd7k2kujec3gpwwa

Leveraging Pruning Techniques for Improving Generalized HMM Decoding in Gene Classification

Mohamed H Ibrahim, Ahmed M Khedr
2018 International Journal of Biomedical Data Mining  
Gene sequence classification is a well-known problem that impacts several sub-disciplines of Bioinformatics including functional genomics and gene expression data analysis.  ...  Unlike standard decoding methods, a paradigm shift from screening to-wards recognition is first performed to integrate all considered models into a combined state space.  ...  Recognition: Recognition tasks usually consist of the discrimination of multiple pattern e.g genes families, so several HMMs are established.  ... 
doi:10.4172/2090-4924.1000133 fatcat:33gcq3jylvcf5eggu4qdrlfoum

Finding Genes by Hidden Markov Models with a Protein Motif Dictionary

Kiyoshi Asai, Tetsushi Yada, Katunobu Itou
1996 Genome Informatics Series  
A new method for combining protein motif dictionary to gene finding system is proposed. The system consists of Hidden Markov Models (HMMs) and a dictionary.  ...  Using the same kind of technique of speech recognition by HMMs with a word dictionary and a grammar, the stochastic network of 'words' enables the motif dictionary to be used during the parsing of the  ...  This means we can parse the whole DNA sequence by the combined HMMs using a dynamic programming algorithm (Baum-Welch algorithm).  ... 
doi:10.11234/gi1990.7.88 fatcat:vdycwpuol5ebfgderwc5iofaki

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)  
This includes a brief description of the classical and computational intelligence methods before discussing their applications to gene finding.  ...  Many of the current gene-finding methods employ computational intelligence techniques that are known to be more robust when dealing with uncertainty and imprecision.  ...  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


The matter of gene prediction, alongside the problems concerned in it, is initially described.  ...  An outsized large of techniques for gene prediction have been developed over the past few years.  ...  A novel method for predicting genes by combining the prediction results of three gene-finding program was developed in 2007.  ... 
doi:10.6084/m9.figshare.14938374.v1 fatcat:gpblejfmj5a63c4pvzdbgkieu4

GenEST, a powerful bidirectional link between cDNA sequence data and gene expression profiles generated by cDNA-AFLP

L. Qin
2001 Nucleic Acids Research  
Various novel pathogenicity factors were identified by combining ESTs from the infective stage juveniles with expression profiles of ∼4000 genes in five developmental stages produced by cDNA-AFLP.  ...  We have developed a computer program (GenEST) that predicts the sizes of virtual transcript-derived fragments (TDFs) of in silico-digested cDNA sequences retrieved from databases.  ...  The potential benefits of this combination in gene discovery and functional analysis prompted us to develop a computer program that creates restriction patterns of cDNAs in silico in accordance with the  ... 
doi:10.1093/nar/29.7.1616 pmid:11266565 pmcid:PMC31277 fatcat:xk5plg53ffbehkx2adpwkw5a2e

Automatic Gene Recognition without Using Training Data

Kiyoshi Asai, Yutaka Ueno, Katunobu Itou, Tetsushi Yada
1997 Genome Informatics Series  
of the recognizer by the result of the recognition are repeated.  ...  In this approach, we start from a simple model, which only uses the knowledge of start codons and the stop codons, then the recognition of the DNA sequences by the recognizer and the training of the parameters  ...  , and in part by Real World Computing (RWC) Program of The Ministry of International Trade and Industry of Japan.  ... 
doi:10.11234/gi1990.8.15 fatcat:lcuauczyejf4jdt4uejk5olvzu

Improving gene recognition accuracy by combining predictions from two gene-finding programs

S. Rogic, B.F. F. Ouellette, A. K. Mackworth
2002 Bioinformatics  
New approaches to computational gene-finding are clearly needed. Results: In this paper we have explored the benefits of combining predictions from already existing gene prediction programs.  ...  best result obtained by either of the two programs individually.  ...  This work was founded by a Research Grant from the Natural Sciences and Engineering Research Council of Canada to Alan Mackworth who holds a Canada Research Chair in Artificial Intelligence.  ... 
doi:10.1093/bioinformatics/18.8.1034 pmid:12176826 fatcat:winnehv5eve25nhndm33bb3a6i

Re-programming DNA-binding specificity in zinc finger proteins for targeting unique address in a genome

Abhinav Grover, Akshay Pande, Krishna Choudhary, Kriti Gupta, Durai Sundar
2010 Journal of Systems and Synthetic Biology  
Custom-design of zinc finger proteins with tailor-made specificity is currently limited by the availability of information on recognition helices for all possible DNA targets.  ...  Here, we explore the novel functionality obtained by engineered zinc finger proteins and the computational approaches for prediction of recognition helices of zinc finger proteins that can raise our ability  ...  Acknowledgments KC and KG were recipients of the Summer Undergraduate Research Award (SURA) from IIT Delhi and DS was supported by a grant from the Department of Biotechnology (DBT), Govt. of India under  ... 
doi:10.1007/s11693-011-9077-4 pmid:22132059 pmcid:PMC3065587 fatcat:ldcs67bzvrbtnokf7w7kxf32im

Identifying the 3'-terminal exon in human DNA

J. E. Tabaska, R. V. Davuluri, M. Q. Zhang
2001 Bioinformatics  
Motivation: We present JTEF, a new program for finding 3 terminal exons in human DNA sequences.  ...  This program is based on quadratic discriminant analysis, a standard nonlinear statistical pattern recognition method.  ...  ACKNOWLEDGEMENTS This work was supported by a grant from Merck Genome Research Institute and by a grant from NHGRI/NIH.  ... 
doi:10.1093/bioinformatics/17.7.602 pmid:11448878 fatcat:ygi7htvuozhurcwzrtzyhasyiu

Combinatorial approaches to gene recognition

M.A. Roytberg, T.V. Astakhova, M.S. Gelfand
1997 Computers and Chemistry  
Recognition of genes via exon assembly approaches leads naturally to the use of dynamic programming.  ...  ; context-dependent schemes for scoring exons and related procedures for exon filtering; and highly specific recognition of arbitrary gene segments, oligonucleotide probes and polymerase chain reaction  ...  We are grateful to SmithKline Beecham and DOE for support of our trip to the Gene-Finding and Gene Recognition Workshop and to J. Fickett and D. Searls for help in arranging the trip.  ... 
doi:10.1016/s0097-8485(96)00034-4 pmid:9440930 fatcat:z6l33oz4prhjdml6wjmjsw6i64
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