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Using a VOM model for reconstructing potential coding regions in EST sequences

Armin Shmilovici, Irad Ben-Gal
2007 Computational statistics (Zeitschrift)  
This paper presents a method for annotating coding and noncoding DNA regions by using variable order Markov (VOM) models.  ...  The paper presents a modified VOM model for detecting and correcting insertion and deletion sequencing errors that are commonly found in ESTs.  ...  This result indicates that VOM based correction outperforms 8 the dynamic programming error-correction algorithm presented in Xu et al. (1995) .  ... 
doi:10.1007/s00180-007-0021-8 fatcat:wova757tmfgjhkldhfqnuqq6si

Identification of coding regions in genomic DNA sequences: an application of dynamic programming and neural networks

Eric E. Snyder, Gary D. Stormo
1993 Nucleic Acids Research  
Dynamic programming (DP) is applied to the problem of precisely identifying internal exons and introns in genomic DNA sequences.  ...  In a pilot study, the system has been trained on a set of 56 human gene fragments containing 150 internal exons in a total of 158,691 bps of genomic sequence.  ...  Dynamic programming (DP) is a recursive optimization procedure first used in sequence analysis by Needleman and Wunsch in 1970 [4] .  ... 
doi:10.1093/nar/21.3.607 pmid:8441672 pmcid:PMC309159 fatcat:4achrcwnfrajdobdunrd3wiy6y

RAMICS: trainable, high-speed and biologically relevant alignment of high-throughput sequencing reads to coding DNA

Imogen A. Wright, Simon A. Travers
2014 Nucleic Acids Research  
Current approaches focus on using heuristics to map reads quickly to large genomes, rather than generating highly accurate alignments in coding regions.  ...  This approach facilitates the generation of highly accurate alignments, accounting for the error biases of the sequencing machine used to generate reads, particularly at homopolymer regions.  ...  using a classical dynamic programming approach to discover exons.  ... 
doi:10.1093/nar/gku473 pmid:24861618 pmcid:PMC4117746 fatcat:fxw5u764f5f73o66d3ygldjnaa

DIANA-EST: a statistical analysis

A. G. Hatzigeorgiou, P. Fiziev, M. Reczko
2001 Bioinformatics  
In the second step of the algorithm the ideal chain of the sequence gets aligned-using a dynamic programming approach-with the real score values in order to maximize the overall coding score potential  ...  Xu et al. (1995) used hexamer in frame occurrences to predict the coding frame and dynamic programming to locate the exact position of the errors.  ...  For 101 out of the 109 sequences that contain coding regions the program was able to detect the correct coding strand.  ... 
doi:10.1093/bioinformatics/17.10.913 pmid:11673235 fatcat:g326spouuvghzjgu4fgk2tmghy

Gene-Finding Approaches for Eukaryotes

G. D. Stormo
2000 Genome Research  
One approach uses protein homology exclu-sively to identify probable coding regions in genomic DNA (Gelfand et al. 1996) . EST and cDNA databases can be used similarly.  ...  Dynamic programming approaches are used on a wide variety of sequence analysis problems, such as sequence alignment, RNA structure prediction, and others (for examples, see Sankoff and Kruskal 1983) .  ... 
doi:10.1101/gr.10.4.394 pmid:10779479 fatcat:xxyarbkpe5gedpfrdyg762mudi

Alignments of DNA and protein sequences containing frameshift errors

Xiaojun Guan, Edward C. Uberbacher
1996 Bioinformatics  
We present a new algorithm which can detect and correct frameshift errors in DNA sequences during comparison of translated sequences with protein sequences in the databases.  ...  Our algorithm uses dynamic programming, producing a guaranteed optimal alignment in the presence of'frameshifts, and has a sensitivity equivalent to Smith-Waterman.  ...  US Department of Energy under contract no. DE-AC05-84OR21400 with Martin Marietta Energy System. Inc.  ... 
doi:10.1093/bioinformatics/12.1.31 fatcat:6wq3m7bosfeinnmmdom2hydofu

Exact mapping of prokaryotic gene starts

M. V. Baytaluk
2002 Briefings in Bioinformatics  
It is known that while the programs used to find genes in prokaryotic genomes reliably map protein-coding regions, they often fail in the exact determination of gene starts.  ...  A dynamic programming algorithm is used to align protein sequences obtained by formal translation of genomic nucleotide sequences. The possibility of frame-shifts is taken into account.  ...  The complete correction list and the alignment procedure are available at http:// bioinform.genetika.ru/genecorrect  ... 
doi:10.1093/bib/3.2.181 pmid:12139437 fatcat:4hd4e5spn5eonpycjoxn6icqe4

Evaluation of the correctable decoding sequencing as a new powerful strategy for DNA sequencing

Chu Cheng, Pengfeng Xiao
2022 Life Science Alliance  
Here, we simulate the sequencing reactions by the self-developed software, and find that this approach has great potential in NGS in terms of sequence decoding, reassembly, error correction, and sequencing  ...  To overcome this limitation, we propose the correctable decoding sequencing strategy, which is a duplex sequencing protocol with conservative theoretical error rates of 0.0009%.  ...  Through dynamic programming, the homopolymer segment is filled in and the remaining parts are used to deduced the base sequence accurately.  ... 
doi:10.26508/lsa.202101294 pmid:35422436 pmcid:PMC9012935 fatcat:5cixddnmkbh2telcr3xnp54aqe

De novo sequencing and variant calling with nanopores using PoreSeq

Tamas Szalay, Jene A Golovchenko
2015 Nature Biotechnology  
Both methods employ a similar error model, but differ in that Loman et 19 al. use only sequence information for the initial pre-assembly error correction, while our 20 approach also uses nanopore current  ...  in the statistical model. 4 The alignment of multiple DNA sequences is a related problem in which various iterative 5 optimization approaches have proven useful 22,23 ; we show here that the same general  ...  is computed using a Smith-Waterman 24style dynamic programming approach.  ... 
doi:10.1038/nbt.3360 pmid:26352647 pmcid:PMC4877053 fatcat:xip7mre4lnf7dd2at3ksxfw42i

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)  
In addition, a long list of available gene finders is compiled.  ...  In this paper, a detailed survey on the existing classical and computational intelligence based methods for gene identification is carried out.  ...  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 Computer Program for Aligning a cDNA Sequence with a Genomic DNA Sequence

Liliana Florea, George Hartzell, Zheng Zhang, Gerald M. Rubin, Webb Miller
1998 Genome Research  
We address the problem of efficiently aligning a transcribed and spliced DNA sequence with a genomic sequence containing that gene, allowing for introns in the genomic sequence and a relatively small number  ...  A freely available computer program, described herein, solves the problem for a 100-kb genomic sequence in a few seconds on a workstation. 3 Corresponding author.  ...  the Adh region.  ... 
doi:10.1101/gr.8.9.967 pmid:9750195 pmcid:PMC310774 fatcat:6uhwp2nrq5asdd2i7m7kecwhie

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).  ...  Experimental results on a newly collected database of human DNA sequences are encouraging, and some new observations about the structure of classifiers for the gene-finding problem have emerged from this  ...  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

ESTScan: a program for detecting, evaluating, and reconstructing potential coding regions in EST sequences

C Iseli, C V Jongeneel, P Bucher
1999 Proceedings. International Conference on Intelligent Systems for Molecular Biology  
In the framework of genome sequencing projects, ESTScan could become a very useful tool for gene discovery, for quality control, and for the assembly of contigs representing the coding regions of genes  ...  We introduce a new type of hidden Markov model that explicitly deals with the possibility of errors in the sequence to analyze, and incorporates a method for correcting these errors.  ...  On the other hand, it can be used in batch mode to scan arbitrarily large numbers of sequences and produce databases of error-corrected coding regions or of predicted protein sequences.  ... 
pmid:10786296 fatcat:ruuu6fj4qndfrj7jnthdi5dgh4

De novo assembly of the carrot mitochondrial genome using next generation sequencing of whole genomic DNA provides first evidence of DNA transfer into an angiosperm plastid genome

Massimo Iorizzo, Douglas Senalik, Marek Szklarczyk, Dariusz Grzebelus, David Spooner, Philipp Simon
2012 BMC Plant Biology  
The scope of this study was to develop an approach for de novo assembly of the carrot mitochondrial genome using next generation sequence data from total genomic DNA.  ...  The approach used here could be used more broadly to sequence and assemble mitochondrial genomes of diverse species.  ...  After mapping, 40 errors were corrected, 6 in coding and 34 in non-coding regions, for a total length of 102 nt and an error rate of 1.14%.  ... 
doi:10.1186/1471-2229-12-61 pmid:22548759 pmcid:PMC3413510 fatcat:4vawttpwpbccjowmr6n2hreqdm

GeneBuilder: interactive in silico prediction of gene structure

L. Milanesi, D. D'Angelo, I. B. Rogozin
1999 Bioinformatics  
The potential gene structure models are obtained by using a dynamic programming method. The program permits the use of several parameters for gene structure prediction and refinement.  ...  Motivation: Prediction of gene structure in newly sequenced DNA becomes very important in large genome sequencing projects.  ...  In this procedure of revealing errors and then correcting them, we use dicodon potential and homology with a selected protein sequence.  ... 
doi:10.1093/bioinformatics/15.7.612 pmid:10487869 fatcat:rexpymhc2va6pl6wzlpabvsu6y
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