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Computational identification of evolutionarily conserved exons

Adam Siepel, David Haussler
2004 Proceedings of the eighth annual international conference on Computational molecular biology - RECOMB '04  
Here, we apply phylo-HMMs to a restricted version of the gene prediction problem in which individual exons are sought that are evolutionarily conserved across a diverse set of species.  ...  We also discuss the technique, previously used in pairwise gene predictors, of explicitly modeling conserved noncoding sequence to help reduce false positive predictions.  ...  Acknowledgments We thank Webb Miller and Jim Kent for their work on multiple alignment, Mathieu Blanchette for identification of conserved sites, Lior Pachter and Gill Bejerano for stimulating conversations  ... 
doi:10.1145/974614.974638 dblp:conf/recomb/SiepelH04 fatcat:bhhgofiewzhthgifdqquw5u5eu

Systematic Identification and Molecular Characteristics of Long Noncoding RNAs in Pig Tissues

Yalan Yang, Rong Zhou, Shiyun Zhu, Xunbi Li, Hua Li, Hui Yu, Kui Li
2017 BioMed Research International  
Conservation analysis revealed that most lncRNAs were evolutionarily conserved among pigs, humans, and mice, such as CUFF.253988.1, which shares homology with human long noncoding RNA MALAT1.  ...  The guanine-cytosine (GC) content of the protein-coding exons and introns was significantly higher than that of the lncRNAs.  ...  The funders had no role in the design, execution, analysis and interpretation of the data, or writing of the study.  ... 
doi:10.1155/2017/6152582 pmid:29062838 pmcid:PMC5618743 fatcat:3e54e5znujg3fniosbi3fptpdy

eShadow: A Tool for Comparing Closely Related Sequences

I. Ovcharenko
2004 Genome Research  
This work was performed under the auspices of the U.S. Department of Energy by the University of California, Lawrence Livermore National Laboratory Contract No.  ...  ACKNOWLEDGMENTS We thank Lisa Stubbs and Marcelo Nobrega for critical reading of the manuscript, valuable suggestions, and comments. We thank Eddy Rubin for his support in creating this tool.  ...  RESULTS eShadow Computational Design and Visualization Scheme eShadow is an interactive computational tool for aligning, visualizing, and evaluating evolutionarily conservation profiles in multiple and  ... 
doi:10.1101/gr.1773104 pmid:15173121 pmcid:PMC419798 fatcat:h4crirmgvfdvrbd7vo5or4pihy

SVC: structured visualization of evolutionary sequence conservation

S. Roepcke, P. Fiziev, P. H. Seeburg, M. Vingron
2005 Nucleic Acids Research  
The visualization on the SVC server provides detailed information about evolutionarily conserved features of these genes.  ...  When these sequences are mapped back onto their encoding exons in the genomes, a scaffold of the conserved gene structure naturally emerges.  ...  The purpose of this step is the identification of alternative and conserved exons that were observed in one organism but not in the other.  ... 
doi:10.1093/nar/gki589 pmid:15991338 pmcid:PMC1160265 fatcat:xb6gjegylbhgzi2j445bxfqhd4

Comparative genomic tools and databases: providing insights into the human genome

Len A. Pennacchio, Edward M. Rubin
2003 Journal of Clinical Investigation  
and Alignment by Hashing Algorithm (SSAHA); conserved noncoding sequence 1 (CNS1); stem cell leukemia (SCL).  ...  Rubin) through the US Department of Energy under contract no. DE-AC03-76SF00098.  ...  Gene identification One of the clear utilities of comparative sequence analysis is for exon and gene identification.  ... 
doi:10.1172/jci200317842 pmid:12697725 pmcid:PMC152942 fatcat:q6h4fst5vrahbbuaiwnikanesa

Comparative genomic tools and databases: providing insights into the human genome

Len A. Pennacchio, Edward M. Rubin
2003 Journal of Clinical Investigation  
and Alignment by Hashing Algorithm (SSAHA); conserved noncoding sequence 1 (CNS1); stem cell leukemia (SCL).  ...  Rubin) through the US Department of Energy under contract no. DE-AC03-76SF00098.  ...  Gene identification One of the clear utilities of comparative sequence analysis is for exon and gene identification.  ... 
doi:10.1172/jci17842 pmid:12697725 pmcid:PMC152942 fatcat:t5efkaqoxnekdbottl5wkmbyqe

Sequence conservation, relative isoform frequencies, and nonsense-mediated decay in evolutionarily conserved alternative splicing

D. Baek, P. Green
2005 Proceedings of the National Academy of Sciences of the United States of America  
To help address these issues, we have constructed and analyzed a large data set of 1,478 exon-skipping alternative splicing (AS) variants evolutionarily conserved in human and mouse.  ...  cases involve a conserved exon whose apparent sole purpose is to mediate destruction of the message when included.  ...  Here, we attempt a more detailed characterization of evolutionarily conserved AS.  ... 
doi:10.1073/pnas.0506139102 pmid:16123126 pmcid:PMC1192826 fatcat:xf7hkn4kyrdwxfzwi4nmk6dlbu

Phylogenetic Shadowing of Primate Sequences to Find Functional Regions of the Human Genome

D. Boffelli
2003 Science  
This approach enabled the localization of regions of collective variation and complementary regions of conservation, facilitating the identification of coding as well as noncoding functional regions.  ...  the evaluation of more evolutionarily distant species.  ...  The primate sequence comparisons illustrate the effectiveness of phylogenetic shadowing in yielding a precise identification of the exon boundaries.  ... 
doi:10.1126/science.1081331 pmid:12610304 fatcat:5cge6lmeknhmpo7d2ssels7tqi

Identification and analysis of alternative splicing events conserved in human and mouse

G. W. Yeo, E. Van Nostrand, D. Holste, T. Poggio, C. B. Burge
2005 Proceedings of the National Academy of Sciences of the United States of America  
Here we describe sequence features that distinguish exons subject to evolutionarily conserved AS, which we call alternative conserved exons (ACEs), from other orthologous human͞ mouse exons and integrate  ...  Our results also imply that the vast majority of AS events represented in the human EST database are not conserved in mouse. exon skipping ͉ regulatory element ͉ cassette exon ͉ transcriptome ͉ comparative  ...  .), a grant from the National Institutes of Health (to C.B.B.), and a Lee Kuan-Yew Graduate Fellowship from Singapore (to G.W.Y.).  ... 
doi:10.1073/pnas.0409742102 pmid:15708978 pmcid:PMC548664 fatcat:yzvn4sd7uremrnsbnatr3rrsym

Characterization and predictive discovery of evolutionarily conserved mammalian alternative promoters

D. Baek, C. Davis, B. Ewing, D. Gordon, P. Green
2007 Genome Research  
Results and Discussion Identification of evolutionarily conserved APs and SPs Using genomic alignments of cDNAs and ESTs and the transcription start-site database DBTSS (Suzuki et al. 2002) , we identified  ...  Sequence conservation in APs and SPs Studies of evolutionarily conserved alternative splicing have found higher sequence conservation in alternatively spliced exons and their flanking introns relative  ... 
doi:10.1101/gr.5872707 pmid:17210929 pmcid:PMC1781346 fatcat:nnfvgames5ephi7j2cn2zgxfwy

Low conservation and species-specific evolution of alternative splicing in humans and mice: comparative genomics analysis using well-annotated full-length cDNAs

Jun-ichi Takeda, Yutaka Suzuki, Ryuichi Sakate, Yoshiharu Sato, Masahide Seki, Takuma Irie, Nono Takeuchi, Takuya Ueda, Mitsuteru Nakao, Sumio Sugano, Takashi Gojobori, Tadashi Imanishi
2008 Nucleic Acids Research  
Of the 20 392 total human AS variants, however, 59% consisted of all conserved exons.  ...  The alignment of the human and mouse genomes showed that 86% of 199 426 total exons in human AS variants were conserved in the mouse genome.  ...  Wakaguri for their technical support during the computational analysis and are grateful to all who annotated the full-length human cDNAs at the H-Inv and H-Inv 2 conferences.  ... 
doi:10.1093/nar/gkn677 pmid:18838389 pmcid:PMC2582632 fatcat:4wfphimgnrfkjfwg7haptrtdy4

Cross-Species Sequence Comparisons: A Review of Methods and Available Resources

K. A. Frazer
2003 Genome Research  
With the availability of whole-genome sequences for an increasing number of species, we are now faced with the challenge of decoding the information contained within these DNA sequences.  ...  Comparative analysis of DNA sequences from multiple species at varying evolutionary distances is a powerful approach for identifying coding and functional noncoding sequences, as well as sequences that  ...  Using these stringent criteria for defining sequences as evolutionarily conserved results in the identification of fewer conserved noncoding sequences, but those identified are more likely to be present  ... 
doi:10.1101/gr.222003 pmid:12529301 pmcid:PMC430969 fatcat:p3vmc5t3hneede3coydo4fn5mm

Identification and characterization of evolutionarily conserved alternative splicing events in a mangrove genus Sonneratia

Yuchen Yang, Wuxia Guo, Xu Shen, Jianfang Li, Shuhuan Yang, Sufang Chen, Ziwen He, Renchao Zhou, Suhua Shi
2018 Scientific Reports  
Among the four species, 1,355 evolutionarily conserved AS (ECAS) events were identified from 1,170 genes.  ...  (2) What are the features of the ECAS events compared with non-evolutionarily conserved AS (non-ECAS) events? and (3) What are the putative functions of the genes containing ECAS events?  ...  Identification of evolutionarily conserved alternative splicing (ECAS) events in Sonneratia. The overall statistics of shared/unique AS events for the four Sonneratia species are shown in Fig. 3 .  ... 
doi:10.1038/s41598-018-22406-6 pmid:29535339 pmcid:PMC5849712 fatcat:rziosbv64zdqpaiev23iqp3b2y

Identification and evolutionary analysis of novel exons and alternative splicing events using cross-species EST-to-genome comparisons in human, mouse and rat

Feng-Chi Chen, Chuang-Jong Chen, Jar-Yi Ho, Trees-Juen Chuang
2006 BMC Bioinformatics  
The identified exons represent not only novel exons but also evolutionarily meaningful AS events that are not previously annotated.  ...  Here we describe a cross-species EST-to-genome comparison algorithm (ENACE) that can identify novel exons for EST-scanty species and distinguish conserved and lineage-specific exons.  ...  Alice Lin-Tsing Yu for supply of human cell lines and tissues; and Dr. Kuo-I Lin, Dr. Chia-Ning Shen, Dr. Ying-Ta Wu, and Dr. Cheng-Chung Liu for supply of mouse cell lines.  ... 
doi:10.1186/1471-2105-7-136 pmid:16536879 pmcid:PMC1479377 fatcat:pzc3hgra7rg3zdnktdvjib2r4e

Genomic Selection Identifies Vertebrate Transcription Factor Fezf2 Binding Sites and Target Genes

Lishan Chen, Jiashun Zheng, Nan Yang, Hao Li, Su Guo
2011 Journal of Biological Chemistry  
Fezf2-bound fragments were enriched for conserved sequences. Surprisingly, ϳ20% of these fragments overlapped well annotated proteincoding exons.  ...  B, occurrence of core binding sites in 1, 2, 3, and 4 or greater copies. C, percent of unique fragments that are evolutionarily conserved between zebrafish and human.  ...  Computational analyses uncovered a consensus core Fezf2 DNA binding site, which subsequently led to the identification of response elements in the selected genomic fragments.  ... 
doi:10.1074/jbc.m111.236471 pmid:21471212 pmcid:PMC3099680 fatcat:5sqojkurtbfivlundxoamqpxza
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