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New Genome Similarity Measures based on Conserved Gene Adjacencies

Daniel Doerr, Luis Antonio B. Kowada, Eloi Araujo, Shachi Deshpande, Simone Dantas, Bernard M.E. Moret, Jens Stoye
2017 Journal of Computational Biology  
Such methods are called gene family-free. In this article, we study an intermediate approach between family-based and family-free genomic similarity measures.  ...  One speaks of gene families, and comparative genomic methods that allow this kind of input are called gene family-based.  ...  We first define three new genome similarity measures based on conserved gene adjacencies (Section 2), followed by some pointers to related literature (Section 3).  ... 
doi:10.1089/cmb.2017.0065 pmid:28590847 fatcat:5piz4c4qwncetcaspzc5ng3t6u

The Potential of Family-Free Genome Comparison [chapter]

Marília D. V. Braga, Cedric Chauve, Daniel Doerr, Katharina Jahn, Jens Stoye, Annelyse Thévenin, Roland Wittler
2013 Models and Algorithms for Genome Evolution  
We study the potential of several family-free approaches in detecting conserved structures, genome rearrangements and in reconstructing ancestral gene orders.  ...  Many methods in computational comparative genomics require gene family assignments as a prerequisite.  ...  of ancestral genomes, employing different gene similarity measures (based on alignment scores, functional similarity, etc).  ... 
doi:10.1007/978-1-4471-5298-9_13 fatcat:2rl74rvbpbgmbheisbixgrqbby

Gene family assignment-free comparative genomics

Daniel Doerr, Annelyse Thévenin, Jens Stoye
2012 BMC Bioinformatics  
As a case study, we present a new similarity measure between pairs of genomes that is related to the breakpoint distance. We propose an exact and a heuristic algorithm for its computation.  ...  Since such information is hard to obtain, it is common to predict homologous groups based on sequence similarity. These hypothetical groups of homologous genes are called gene families.  ...  In support of our case, we present a new approach to calculate the number of conserved adjacencies, which is a similarity measure related to the breakpoint distance, without the use of gene families.  ... 
doi:10.1186/1471-2105-13-s19-s3 pmid:23281826 pmcid:PMC3526435 fatcat:ydnaay67w5bc7geypzikzhfbv4

A new measurement of sequence conservation

Xiaohui Cai, Haiyan Hu, Xiaoman Li
2009 BMC Genomics  
To identify both discontiguously and contiguously conserved regions, we proposed a new measurement of sequence conservation, which measures sequence similarity based only on the conserved segments within  ...  It is critical to have a new measurement of sequence conservation that is based only on the conserved segments in one region.  ...  Results Our new measurement of sequence conservation calculates the sequence similarity based on conserved segments.  ... 
doi:10.1186/1471-2164-10-623 pmid:20028539 pmcid:PMC2807881 fatcat:mcs7wsh3abgotlrjks2ld6e5oy

Natural Selection on Gene Order in the Genome Reorganization Process After Whole-Genome Duplication of Yeast

R. P. Sugino, H. Innan
2011 Molecular biology and evolution  
S. cerevisiae have experienced a whole-genome duplication followed by an extensive reorganization process of gene order, during which a number of new adjacent gene pairs appeared.  ...  A genome must locate its coding genes on the chromosomes in a meaningful manner with the help of natural selection, but the mechanism of gene order evolution is poorly understood.  ...  The similarity score was measured by Pearson's correlation coefficient (r ).  ... 
doi:10.1093/molbev/msr118 pmid:21546358 fatcat:ivopxzwdsbhxroumri735rpxda

Transcription unit conservation in the three domains of life: a perspective from Escherichia coli

G Moreno-Hagelsieb
2001 Trends in Genetics  
Our computer analyses were based on the comparison of the conservation of adjacent pairs of genes transcribed in the same direction in E. coli.  ...  We measure co-occurrence as the number of pairs of adjacent genes where both genes have an ortholog in the genome of interest, normalized against the sum of such pairs and pairs where only one of the genes  ... 
doi:10.1016/s0168-9525(01)02241-7 pmid:11275307 fatcat:26lds3u7nfa63hldzdxkckpqta

A novel method for accurate operon predictions in all sequenced prokaryotes

M. N. Price
2005 Nucleic Acids Research  
We combine comparative genomic measures and the distance separating adjacent genes to predict operons in 124 completely sequenced prokaryotic genomes.  ...  conserved operons; and Synechocystis PCC 6803 has many operons even though it has unusually wide spacings between conserved adjacent genes.  ...  Richard Bonneau, Tracy Nicholson and Richard Stephens for providing unpublished microarray data, Inna Dubchak for insightful discussions and sharing resources, and the rest of the Arkin lab for comments on  ... 
doi:10.1093/nar/gki232 pmid:15701760 pmcid:PMC549399 fatcat:r3ekibl3abfctl274qnbjebeye

Similar Evolutionary Trajectories for Retrotransposon Accumulation in Mammals

Reuben M. Buckley, R. Daniel Kortschak, Joy M. Raison, David L. Adelson
2017 Genome Biology and Evolution  
Through conservation of synteny, gene regulation and nuclear organization, mammalian genomes with dissimilar retrotransposons follow similar evolutionary trajectories.  ...  This suggested a similar evolutionary interaction between retrotransposon activity and conserved genome architecture across our species.  ...  (a) Top 10% of genome segments based on retrotransposon density of new SINEs and new L1s. (b) Top 10% of genome segments based on retrotransposon density of ancient elements and old L1s.  ... 
doi:10.1093/gbe/evx179 pmid:28945883 pmcid:PMC5610350 fatcat:4f2xe7im4nbgha2nlop63cw2dq

Comprehensive Analysis of Replication Origins in Saccharomyces cerevisiae Genomes

Dan Wang, Feng Gao
2019 Frontiers in Microbiology  
Furthermore, we found the genes adjacent to conserved ARSs are significantly enriched in DNA binding, enzyme activity, transportation, and energy, whereas for the genes adjacent to non-conserved ARSs are  ...  Subsequently, we built a non-redundant dataset with a total of 520 ARSs, which are based on ARSs annotation of S. cerevisiae S288C from SGD and then supplemented with those from OriDB and DeOri databases  ...  Based on the homologous ARSs of various yeast strains, we extracted their adjacent genes from the corresponding yeast genomes.  ... 
doi:10.3389/fmicb.2019.02122 pmid:31572328 pmcid:PMC6753640 fatcat:guvrjuijrzfujanfarapuy2kb4

Characterization of relationships between transcriptional units and operon structures in Bacillus subtilis and Escherichia coli

Shujiro Okuda, Shuichi Kawashima, Kazuo Kobayashi, Naotake Ogasawara, Minoru Kanehisa, Susumu Goto
2007 BMC Genomics  
To understand the relationships between TUs and operons, we defined a new classification system for adjacent gene pairs, divided into three groups according to the level of gene co-regulation: operon pairs  ...  Additional analysis revealed that they were also correlated to the levels of conservation across about 200 prokaryotic genomes.  ...  The computational resources were provided by the Bioinformatics Center, Institute for Chemical Research, Kyoto University and the Super Computer System, Human Genome Center, The Institute of Medical Science  ... 
doi:10.1186/1471-2164-8-48 pmid:17298663 pmcid:PMC1808063 fatcat:oefugs6z6zf55lhgu3bcjjlkbq

Operon prediction using both genome-specific and general genomic information

Phuongan Dam, Victor Olman, Kyle Harris, Zhengchang Su, Ying Xu
2006 Nucleic Acids Research  
Our analyses have led to a number of new insights about operon prediction, including that (i) different features have different levels of discerning power when used on adjacent gene pairs with different  ...  Based on these new insights, our newly developed operon-prediction program achieves more accurate operon prediction than the previous ones, and it uses features that are most readily available from genomic  ...  We have previously developed a scoring scheme for measuring the GO-based functional similarity between a pair of genes (20) .  ... 
doi:10.1093/nar/gkl1018 pmid:17170009 pmcid:PMC1802555 fatcat:cfchujw3dfh63i3lzrr3pl2pva

The gene family-free median of three

Daniel Doerr, Metin Balaban, Pedro Feijão, Cedric Chauve
2017 Algorithms for Molecular Biology  
sequence similarity in the score of a gene adjacency.  ...  The gene family-free framework for comparative genomics aims at providing methods for gene order analysis that do not require prior gene family assignment, but work directly on a sequence similarity graph  ...  genomes are connected by a strictly positively weighted edge according to gene similarity measure σ.  ... 
doi:10.1186/s13015-017-0106-z pmid:28559921 pmcid:PMC5446766 fatcat:zr2bztiwujbmjfirhg5log6mki

The Gene Family-Free Median of Three [chapter]

Daniel Doerr, Pedro Feijão, Metin Balaban, Cedric Chauve
2016 Lecture Notes in Computer Science  
sequence similarity in the score of a gene adjacency.  ...  The gene family-free framework for comparative genomics aims at providing methods for gene order analysis that do not require prior gene family assignment, but work directly on a sequence similarity graph  ...  genomes are connected by a strictly positively weighted edge according to gene similarity measure σ.  ... 
doi:10.1007/978-3-319-43681-4_9 fatcat:qifvnbkwvrf4ldvu3ij3gfhspa

The gene family-free median of three [article]

Daniel Doerr, Pedro Feijao, Metin Balaban, Cedric Chauve
2016 arXiv   pre-print
similarity in the score of a gene adjacency.  ...  The gene family-free framework for comparative genomics aims at developing methods for gene order analysis that do not require prior gene family assignment, but work directly on a sequence similarity multipartite  ...  In subsequent analyses, gene similarities are based on local alignment hits identified with BLASTP [2] on protein sequences using an e-value threshold of 10 −5 .  ... 
arXiv:1606.05910v1 fatcat:ue3e5kvtbjchrjgh6mtf6nwgju

Genome Compaction and Stability in Microsporidian Intracellular Parasites

Claudio H Slamovits, Naomi M Fast, Joyce S Law, Patrick J Keeling
2004 Current Biology  
The degree of conservation therefore, paradoxically composed of rapidly evolving of gene order between A. locustae and E. cuniculi was sequences harbored within a slowly evolving genome, measured as the  ...  To explore the effects of compaction on nuclear significant similarity to E. cuniculi homologs, three show genome evolution, we sequenced 685,000 bp of the significant similarity to homologs in other organisms  ...  significant conservation of gene by using marker-based methods[30].  ... 
doi:10.1016/j.cub.2004.04.041 pmid:15186746 fatcat:yotkto2byba2bcft4k5b3jzixi
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