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On the inversion-indel distance

Eyla Willing, Simone Zaccaria, Marília DV Braga, Jens Stoye
2013 BMC Bioinformatics  
and deletions and is called the inversion-indel distance.  ...  , the inversionindel distance is equal to the DCJ-indel distance.  ...  Acknowledgements The authors would like to thank Paola Bonizzoni for suggestions how to improve the presentation of the proof of Theorem 3.  ... 
doi:10.1186/1471-2105-14-s15-s3 pmid:24564182 pmcid:PMC3851949 fatcat:3dih7qf34rfl7nvkqntyu5254i

Restricted DCJ-Indel Model Revisited [chapter]

Marília D. V. Braga, Jens Stoye
2013 Lecture Notes in Computer Science  
(BMC Bioinformatics 13, Suppl. 19, S14), but only an upper bound for the restricted DCJ-indel distance was provided.  ...  DCJ-indel models.  ...  Acknowledgments MDVB is funded by the Brazilian research agency CNPq grant PROMETRO 563087/10-2.  ... 
doi:10.1007/978-3-319-02624-4_4 fatcat:wavtm5iu4vhtvfa6n4glejfhdu

Restricted DCJ-indel model: sorting linear genomes with DCJ and indels

Poly H da Silva, Raphael Machado, Simone Dantas, Marília DV Braga
2012 BMC Bioinformatics  
We then develop a sorting algorithm and give a tight upper bound for the restricted DCJ-indel distance. Conclusions: We have given a tight upper bound for the restricted DCJ-indel distance.  ...  The question whether this bound can be reduced so that both the general and the restricted DCJ-indel distances are equal remains open.  ...  This article has been published as part of BMC Bioinformatics Volume 13 Supplement 19, 2012: Proceedings of the Tenth Annual Research in Computational Molecular Biology (RECOMB) Satellite Workshop on Comparative  ... 
doi:10.1186/1471-2105-13-s19-s14 pmid:23281630 pmcid:PMC3526439 fatcat:qsgjgdfr3bgblnoza2lnfeltqq

Comparative and Phylogenetic Analysis of the Complete Chloroplast Genome of Santalum (Santalaceae)

Xiaojin Liu, Daping Xu, Zhou Hong, Ningnan Zhang, Zhiyi Cui
2021 Forests  
Three mutation hotspot regions, 14 small inversions, and 460 indels events were discovered in the Santalum chloroplast genome.  ...  The whole set of ndh genes and the infA gene were found to lose their functions. The P-distance among the Santalum species was 0.0003 to 0.00828.  ...  Data Availability Statement: The 12 newly assembled chloroplast genomes were deposited in GenBank under the accession numbers of MW464914 to MW464925.  ... 
doi:10.3390/f12101303 fatcat:ksk4dkuyvvh4fah62i7mqbia2a

On the weight of indels in genomic distances

Marília D V Braga, Raphael Machado, Leonardo C Ribeiro, Jens Stoye
2011 BMC Bioinformatics  
Conclusions: We show that the proposed framework establishes the triangular inequality in both distances, by summing a surcharge on indel operations and on substitutions that depends only on the number  ...  Classical approaches to compute the genomic distance are usually limited to genomes with the same content, without duplicated markers.  ...  Observe that m id depends only on the DCJ-indel distance and the number of unique markers.  ... 
doi:10.1186/1471-2105-12-s9-s13 pmid:22151784 pmcid:PMC3283315 fatcat:n5axgbxfb5by5oyoajs7flchze

The Drosophila Genome Nexus: A Population Genomic Resource of 623 Drosophila melanogaster Genomes, Including 197 from a Single Ancestral Range Population

Justin B. Lack, Charis M. Cardeno, Marc W. Crepeau, William Taylor, Russell B. Corbett-Detig, Kristian A. Stevens, Charles H. Langley, John E. Pool
2015 Genetics  
We evaluated variations and extensions of this approach and settled on an assembly strategy that utilizes two alignment programs and incorporates both substitutions and short indels to construct an updated  ...  The large sample size, high genetic diversity, and potentially simpler demographic history of the DPGP3 sample will make this a highly valuable resource for fundamental population genetic research.  ...  Emerson for packaging the admixture HMM method; Isaac Knoflicek for help with data management and the DGN web site; and the University of Wisconsin Center for High Throughput Computing for computational  ... 
doi:10.1534/genetics.115.174664 pmid:25631317 pmcid:PMC4391556 fatcat:mcxnxawuuvan5jbo3t2rjtgls4

Chromosomal character optimization

Ward C. Wheeler
2007 Molecular Phylogenetics and Evolution  
A method is presented to optimize chromosomal data on a cladogram.  ...  Locus labeling is not a requirement of the procedure and such annotation will result from the dynamic homology analysis of the chromosome data.  ...  good artwork (as opposed to the rest); and the National Science Foundation and National Aeronautics and Space Agency for research support.  ... 
doi:10.1016/j.ympev.2007.01.010 pmid:17363286 fatcat:wyimy2xdyzgzhf3mgvyfk3vo3i

Nucleotide substitution rates of diatom plastid encoded protein genes are positively correlated with genome architecture

Yan Ren, Mengjie Yu, Wai Yee Low, Tracey A. Ruhlman, Nahid H. Hajrah, Abdelfatteh El Omri, Mohammad K. Alghamdi, Mumdooh J. Sabir, Alawiah M. Alhebshi, Majid R. Kamli, Jamal S. M. Sabir, Edward C. Theriot (+2 others)
2020 Scientific Reports  
Significant positive correlations were identified between substitution rates and measures of genomic rearrangements, including indels and inversions, which is a similar result to what was found in legume  ...  As one of the single-celled photosynthetic organisms that inhabit marine, aquatic and terrestrial ecosystems, diatoms contribute ~ 45% of global primary production.  ...  UT Austin for access to supercomputers and Erika Schwarz, Mao-Lun Weng and Jin Zhang for advice on rate analyses.  ... 
doi:10.1038/s41598-020-71473-1 pmid:32873883 pmcid:PMC7462845 fatcat:x7vo4fbxzjh77pw4maxp74z4uq

Evolutionary directions of single nucleotide substitutions and structural mutations in the chloroplast genomes of the family Calycanthaceae

Wenpan Dong, Chao Xu, Jun Wen, Shiliang Zhou
2020 BMC Evolutionary Biology  
Of the structural mutations, indels and repeats had obvious directions, but microsatellites and inversions were non-directional. Structural mutations increased the single nucleotide mutations rates.  ...  However, there are no empirical observations on the patterns, directions, and mutation rates, which are the key topics in chloroplast genome evolution.  ...  The distances are based on SNPs.  ... 
doi:10.1186/s12862-020-01661-0 pmid:32736519 fatcat:wk7cirraojd5dhbk2l63trnfli

Natural variation in genome architecture among 205 Drosophila melanogaster Genetic Reference Panel lines

W. Huang, A. Massouras, Y. Inoue, J. Peiffer, M. Ramia, A. M. Tarone, L. Turlapati, T. Zichner, D. Zhu, R. F. Lyman, M. M. Magwire, K. Blankenburg (+39 others)
2014 Genome Research  
Our cytogenetic analysis identified 16 polymorphic inversions in the DGRP.  ...  . , 2011 , which have a different spectrum of allelic effects than SNPs and small insertions and deletions (indels).  ...  Acknowledgments The work was supported by NIH grants NHGRI U54 HG003273  ... 
doi:10.1101/gr.171546.113 pmid:24714809 pmcid:PMC4079974 fatcat:yhzg432rmrcflgwhanzoxeikem

Evolution and genome specialization of Brucella suis biovar 2 Iberian lineages

Ana Cristina Ferreira, Rogério Tenreiro, Maria Inácia Corrêa de Sá, Ricardo Dias
2017 BMC Genomics  
Besides the 210 kb translocation event present in all biovar 2 strains, an inversion with 944 kb was presented in chromosome I of strains from the Iberian clone.  ...  Molecular identification of both B. suis biovar 2 clonal lineages could be easily achieved using the target-PCR procedures established in this work for the evaluated INDELs.  ...  The datasets used and/or analysed during the current study are available from the corresponding author on reasonable request. The authors declare that they have no competing interests.  ... 
doi:10.1186/s12864-017-4113-8 pmid:28899413 pmcid:PMC5596481 fatcat:dtc4p4btdzfg3ol6ntsqvbzii4

Small Parsimony for Natural Genomes in the DCJ-Indel Model [article]

Daniel Doerr, Cedric Chauve
2021 arXiv   pre-print
The problem aims at finding the gene orders at internal nodes of a given phylogenetic tree such that the overall genome rearrangement distance along the tree branches is minimized.  ...  The evolutionary model that we consider is the DCJ-indel model that includes the Double-Cut and Join rearrangement operation and the insertion and deletion of genome segments.  ...  The DCJ-indel distance, given by d DCJ−ID (A, B) = n − c − i 2 + δ, grows inversely to the number c of cycles and twice the number i of paths of odd length in G [7, 10] , where δ denotes the indel penalty  ... 
arXiv:2108.04297v1 fatcat:qxsghaisabgkdirsqloyijoy4i

Molecular population genetics of the OBP83 genomic region in Drosophila subobscura and D. guanche: contrasting the effects of natural selection and gene arrangement expansion in the patterns of nucleotide variation

A Sánchez-Gracia, J Rozas
2010 Heredity  
Chromosomal inversion polymorphism play a major role in the evolutionary dynamics of populations and species because of their effects on the patterns of genetic variability in the genomic regions within  ...  inversions.  ...  Acknowledgements We thank Carmen Segarra for her valuable contribution in performing the in situ hybridization.  ... 
doi:10.1038/hdy.2010.26 pmid:20332808 pmcid:PMC3183857 fatcat:fh2kq77inbblfdvrbtguobsdpa

MoDIL: detecting small indels from clone-end sequencing with mixtures of distributions

Seunghak Lee, Fereydoun Hormozdiari, Can Alkan, Michael Brudno
2009 Nature Methods  
MoDIL represents the random variable of the expected size of indel (mean of insert size minus the mapped distance) with two random variables, one for each haplotype.  ...  Mate pairs are used to locate structural variants by comparing the distance between the mapped locations of the read pairs on a reference genome (mapped distance) and the known insert size.  ... 
doi:10.1038/nmeth.f.256 pmid:19483690 fatcat:a5ymqelsdzbkjlh3nzzancfz5a

MapCaller - An integrated and efficient tool for short-read mapping and variant calling using high-throughput sequenced data [article]

Hsin-Nan Lin, Wen-Lian Hsu
2019 bioRxiv   pre-print
It not only maps every short read onto a reference genome, but it also detects single nucleotide variants, indels, inversions and translocations at the same time.  ...  The identification of personal genome variants using NGS technology is a critical factor for the success of clinical genomics studies.  ...  We describe how the SNVs, indels, inversions and translocations are identified based on the PFM and by Map-Caller below.  ... 
doi:10.1101/783605 fatcat:odcdcf5ryjezpaerjlb464uz44
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