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A Method for Comparing Three Genomes [chapter]

Guilherme P. Telles, Marcelo M. Brigido, Nalvo F. Almeida, Carlos J. M. Viana, Daniel A. S. Anjos, Maria Emilia M. T. Walter
2005 Lecture Notes in Computer Science  
In this work, we propose a method for comparing three genomes simultaneously, at the basic level of their sequences.  ...  We used our method to compare genomes of two pathogenic and five non-pathogenic fungi, and made a biological analysis based on one of these results.  ...  In this work, we propose a method for comparing three genomes simultaneously, at the basic level of their sequences.  ... 
doi:10.1007/11532323_17 fatcat:wb4oaeqadregdnepj6ll5lis3i

Comparative Evaluation of Intron Prediction Methods and Detection of Plant Genome Annotation Using Intron Length Distributions

Long Yang, Hwan-Gue Cho
2012 Genomics & Informatics  
It is suggested that a three-phase evaluation is a fast and effective method of detecting intron annotation problems.  ...  Using two model plant (rice and Arabidopsis) genomes, we compared two well-known intron prediction tools: the Blast-Like Alignment Tool (BLAT) and Sim4cc.  ...  [14] Restauro-G A rapid genome re-annotation system for comparative genomics Tamaki et al.  ... 
doi:10.5808/gi.2012.10.1.58 pmid:23105930 pmcid:PMC3475488 fatcat:6w7k6rl2ojeodlrwfsopkk5ksm

Where Are The Genes Missing From Prokaryotic Genomes?

Luciano Brocchieri
2015 Journal of Phylogenetics & Evolutionary Biology  
To facilitate using frame analysis on a genomic scale and extend its usage to sequences of any composition, we recently developed a method for quantifying and generalizing the information provided by frame  ...  periodicity ("Hits") corresponding to S-profile bubbles, looks for associated open reading frames (ORFs), compares them to genome annotations, and displays missing ORFs and corresponding hits together  ...  To facilitate using frame analysis on a genomic scale and extend its usage to sequences of any composition, we recently developed a method for quantifying and generalizing the information provided by frame  ... 
doi:10.4172/2329-9002.1000e114 fatcat:w7sy4pnvpjh4nizmilpy6evyve

GenomeFingerprinter: The Genome Fingerprint and the Universal Genome Fingerprint Analysis for Systematic Comparative Genomics

Yuncan Ai, Hannan Ai, Fanmei Meng, Lei Zhao, Vladimir Brusic
2013 PLoS ONE  
This paper provided a new method for rapidly computing, geometrically visualizing, and intuitively comparing genome sequences at fingerprint level, and hence established a new method of universal genome  ...  comparative genomics (SCG) for comparing in-one-sitting a number of genomes crossing genetic category in diverse strains.  ...  The post-genomic era promoted a huge demand for data mining and robust reasoning with massive genome sequences [1] . So far, there were numerous methods for comparative genomics at small scale.  ... 
doi:10.1371/journal.pone.0077912 pmid:24205026 pmcid:PMC3812135 fatcat:htechvxdzzeetjev2oudgwdnae

A novel clustering method via nucleotide-based Fourier power spectrum analysis

Bo Zhao, Victor Duan, Stephen S.-T. Yau
2011 Journal of Theoretical Biology  
Mathematical moments are calculated for each of these spectra to create a multidimensional vector in a Euclidean space for each gene or genome sequence.  ...  A novel clustering method is proposed to classify genes or genomes.  ...  Acknowledgment Victor Duan would like to thank Shengqiang Xu for helpful discussions about Cþþ programming.  ... 
doi:10.1016/j.jtbi.2011.03.029 pmid:21443881 pmcid:PMC7094093 fatcat:y23wfqfo2bgctckutwlfuxa6n4

Making sense of an alphabet soup: the use of a new bioinformatics tool for identification of novel gene islands. Focus on "Identification of genomic islands in the genome of Bacillus cereus by comparative analysis with Bacillus anthracis"

Amy O. Charkowski
2004 Physiological Genomics  
a relatively low GC content compared with surrounding genes, even in AT-rich genomes.  ...  The most powerful method for identifying HGT is comparison of genomes within a species or genus, but in many cases, only one or a few genome sequences are available so this is not possible.  ... 
doi:10.1152/physiolgenomics.00199.2003 pmid:14726601 fatcat:5xrzil3mvjfevggj42na2ad3za

Computational pan-genome mapping and pairwise SNP-distance improve detection of Mycobacterium tuberculosis transmission clusters

Christine Jandrasits, Stefan Kröger, Walter Haas, Bernhard Y. Renard, Sergei L. Kosakovsky Pond
2019 PLoS Computational Biology  
This study introduces PANPASCO, a computational pan-genome mapping based, pairwise distance method that is highly sensitive to differences between cases, even when located in regions of lineage specific  ...  reference genomes.  ...  Acknowledgments We would like to thank Pascal Wetzel and Julius Tembrockhaus for assistance in carrying out computational pan-genome related experiments and Lena Fiebig and Andrea Sanchini for providing  ... 
doi:10.1371/journal.pcbi.1007527 pmid:31815935 pmcid:PMC6922483 fatcat:smoirlaqvnby5hpqc76lqzm5jm

The society of genes: networks of functional links between genes from comparative genomics

Itai Yanai, Charles DeLisi
2002 Genome Biology  
Comparative genomics provides at least three methods beyond traditional sequence similarity for identifying functional links between genes: the examination of common phylogenetic distributions, the analysis  ...  It therefore shows considerable utility and promise as a tool for understanding genomic structure, and for guiding high throughput experimental investigations.  ...  This work was funded by a Whitaker Graduate Fellowship and by a Koshland Postdoctoral Fellowship to I.Y.  ... 
pmid:12429063 pmcid:PMC133448 fatcat:gcfpctmpxjaw3j6du5zftl6mwq

Controlling for Phylogenetic Relatedness and Evolutionary Rates Improves the Discovery of Associations Between Species' Phenotypic and Genomic Differences

Xavier Prudent, Genis Parra, Peter Schwede, Juliana G. Roscito, Michael Hiller
2016 Molecular biology and evolution  
Here, we present two new Forward Genomics methods that overcome these limitations by (1) directly controlling for phylogenetic relatedness, (2) controlling for differences in evolutionary rates, and (3  ...  These new Forward Genomics methods represent a significant advance in our ability to discover the genomic basis underlying phenotypic differences between species.  ...  Acknowledgments We thank Virag Sharma for help with Mtnr1b mutations, Peter Steinbach and Ulf Markwardt for a fast transalign implementation, David Orme for help with the Caper R package, and the Computer  ... 
doi:10.1093/molbev/msw098 pmid:27222536 pmcid:PMC4948712 fatcat:4htuzhxlwjcftfqbnckajqsrni

Automated Whole-Genome Multiple Alignment of Rat, Mouse, and Human

M. Brudno
2004 Genome Research  
We have built a whole-genome multiple alignment of the three currently available mammalian genomes using a fully automated pipeline that combines the local/global approach of the Berkeley Genome Pipeline  ...  , using predicted exons in the three genomes.  ...  ACKNOWLEDGMENTS We thank the Rat Genome Sequencing Project Consortium for the opportunity to work with the rat genome during the sequencing phases and in the subsequent analysis phase.  ... 
doi:10.1101/gr.2067704 pmid:15060011 pmcid:PMC383314 fatcat:ef2zr77m3fbivnhajtkpk52xuy

A comparative study of single nucleotide variant detection performance using three massively parallel sequencing methods

Linea Christine Trudsø, Jeppe Dyrberg Andersen, Stine Bøttcher Jacobsen, Sofie Lindgren Christiansen, Clàudia Congost-Teixidor, Marie-Louise Kampmann, Niels Morling, Tomohiko Ai
2020 PLoS ONE  
We compared the results of single nucleotide variant (SNV) detection of three MPS methods: WGS, WES, and HaloPlex target enrichment sequencing (HES) using matched DNA of 10 individuals.  ...  Today, multiple approaches for MPS of DNA are available, including targeted gene sequencing (TGS) panels, whole exome sequencing (WES), and whole genome sequencing (WGS).  ...  Acknowledgments We thank Carina Jønck for bioinformatics support, Anja Jørgensen for technical assistance in the laboratory.  ... 
doi:10.1371/journal.pone.0239850 pmid:32986766 fatcat:e24kposnhrbjjm7ncvxshxny6i

A new strategy for better genome assembly from very short reads

Yan Ji, Yixiang Shi, Guohui Ding, Yixue Li
2011 BMC Bioinformatics  
Results: A novel strategy for improving genome assembly from very short reads is proposed.  ...  Because of repetitive regions of genomes and some other factors, assembly of very short reads is still a challenging issue.  ...  For each simulation dataset from a genome, an assembly method or tool gets a rank of 1 to 4 in each category.  ... 
doi:10.1186/1471-2105-12-493 pmid:22208765 pmcid:PMC3268122 fatcat:nkfg2cvnjjhalmnkqqe7pfdpc4

Comparison of Whole Genome Amplification Methods for Further Quantitative Analysis with Microarray-based Comparative Genomic Hybridization

Yun-Shien Lee, Chi-Neu Tsai, Chia-Lung Tsai, Shuenn-Dyh Chang, Ding-Wei Hsueh, Chun-Ting Liu, Chung-Chun Ma, Seng-Hsuan Lin, Tzu-Hao Wang, Hsin-Shih Wang
2008 Taiwanese Journal of Obstetrics & Gynecology  
Chen (Academia Sinica) for comments on statistical analysis, Pei-Tsen Lin (GMRCL) for technical assistance. This study was supported by grants CMRPG360031 (to S.D. Chang), CMRPG340462 (to T.H.  ...  When we used 10 ng of genomic DNA as input to compare DOP-PCR, LM-PCR, and SDA, all three methods yielded sufficient DNA products for subsequent molecular studies, such as microsatellite genotyping, SNP  ...  The available amount of genomic DNA from some clinical specimen is still a limiting factor for genomic analysis with array-CGH.  ... 
doi:10.1016/s1028-4559(08)60052-2 pmid:18400580 fatcat:wuwuozehlzewxa747cndkpnxna

Bayesian prediction of microbial oxygen requirement

Dan B. Jensen, David W. Ussery
2013 F1000Research  
This method further compares the performance of a single-step naive Bayesian prediction of the three included classifications, compared to a simple Bayesian network with two steps.  ...  Here, we describe a method for distinguishing aerobic, anaerobic and facultative anaerobic bacteria, based on genome sequence-derived input, using naive Bayesian inference.  ...  Acknowledgements The authors would like to thank Tammi Vesth for help in this project. Competing interests No competing interests were disclosed.  ... 
doi:10.12688/f1000research.2-184.v1 pmid:26913185 pmcid:PMC4743139 fatcat:mldz7ii64jffdlzdru6zx653wu

IslandViewer update: improved genomic island discovery and visualization

Bhavjinder K. Dhillon, Terry A. Chiu, Matthew R. Laird, Morgan G. I. Langille, Fiona S. L. Brinkman
2013 Nucleic Acids Research  
Many computational tools exist for the prediction of GIs, but three of the most accurate methods are available in integrated form via IslandViewer: IslandPath-DIMOB, SIGI-HMM and IslandPick.  ...  IslandViewer (http://pathogenomics.sfu.ca/island viewer) is a web-accessible application for the computational prediction and analysis of genomic islands (GIs) in bacterial and archaeal genomes.  ...  Center for Biotechnology Information for providing complete genome sequence data, freely available.  ... 
doi:10.1093/nar/gkt394 pmid:23677610 pmcid:PMC3692065 fatcat:3kykn2bxi5ft5pvuebn4cjnqmu
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