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Detecting Repeat Families in Incompletely Sequenced Genomes [chapter]

José Augusto Amgarten Quitzau, Jens Stoye
Lecture Notes in Computer Science  
We present a novel method for repeat family detection and characterization in cases where the target genome sequence is not completely known.  ...  Their detection and analysis pose a number of challenges in genomic sequence analysis, especially if the genome is not completely sequenced.  ...  Conclusion We presented two methods for detecting repeat families in incompletely sequenced genomes.  ... 
doi:10.1007/978-3-540-87361-7_29 fatcat:bko5onlbxnddjkrmym5oyz5fo4

Discovering and detecting transposable elements in genome sequences

C. M. Bergman, H. Quesneville
2007 Briefings in Bioinformatics  
Here we review the diversity of innovative approaches to identify and annotateTEs in the post-genomic era, covering both the discovery of new TE families and the detection of individual TE copies in genome  ...  The contribution of transposable elements (TEs) to genome structure and evolution as well as their impact on genome sequencing, assembly, annotation and alignment has generated increasing interest in developing  ...  The most common strategy is to detect pairs of similar sequences at different locations in a self-genome comparison, and then cluster these pairs to obtain repeat families.  ... 
doi:10.1093/bib/bbm048 pmid:17932080 fatcat:r2cjoizumbczjbwe2oosm6irpi

The Complex Repeats of Dictyostelium discoideum

G. Glockner
2001 Genome Research  
In the course of determining the sequence of the Dictyostelium discoideum genome we have characterized in detail the quantity and nature of interspersed repetitive elements present in this species.  ...  All elements show insertion preference into loci in which other elements of the same family reside.  ...  The publication costs of this article were defrayed in part by payment of page charges.  ... 
doi:10.1101/gr.gr-1622rr pmid:11282973 pmcid:PMC311061 fatcat:w76kxiaxhvgxpeajaavt6f6ywy

The Complex Repeats of Dictyostelium discoideum

Gernot Glöckner, Karol Szafranski, Thomas Winckler, Theodor Dingermann, Michael A. Quail, Edward Cox, Ludwig Eichinger, Angelika Anna Noegel, André Rosenthal
2001 Genome Research  
In the course of determining the sequence of the Dictyostelium discoideum genome we have characterized in detail the quantity and nature of interspersed repetitive elements present in this species.  ...  All elements show insertion preference into loci in which other elements of the same family reside.  ...  The publication costs of this article were defrayed in part by payment of page charges.  ... 
doi:10.1101/gr.162201 fatcat:ixrdxmdoebbbzevjlslz6j2biq

A novel mutation in PRPF31, causative of autosomal dominant retinitis pigmentosa, using the BGISEQ-500 sequencer

2018 International Journal of Ophthalmology  
In all members of Family ONE and Family TWO with available DNA samples, the genetic variant was validated using Sanger sequencing.  ...  Sanger sequencing was performed upon probands, as well as upon other family members. This novel, pathogenic genotype co-segregated with retinitis pigmentosa phenotype in these two families.  ...  The MSR1 element has two forms, 3 repeats and 4 repeats, in human genome. The 4 repeats allele was along with higher expression of PRPF31.  ... 
doi:10.18240/ijo.2018.01.06 pmid:29375987 pmcid:PMC5767654 fatcat:fw4nw67wgbgpvhxym7tozt7uae

CAN—a pan-carnivore SINE family

Nikita S. Vassetzky, Dmitri A. Kramerov
2002 Mammalian Genome  
Here we demonstrate CAN sequences in representatives of all carnivore families, but not beyond carnivores, on the basis of sequence bank search and genomic PCR.  ...  CAN SINEs initially found in American mink were named after dogs (Canis), and the range of their distribution in the genomes of carnivores and mammals in general remained topical.  ...  Full-size CAN sequences were found in the genomic banks of representatives of all carnivore families except civets, where only incomplete sequences were found.  ... 
doi:10.1007/s00335-001-2111-1 pmid:11773970 fatcat:spfuekifajdbhesqxgwoaqrita

The Spin/Ssty repeat: a new motif identified in proteins involved in vertebrate development from gamete to embryo

Eike Staub, Detlev Mennerich, André Rosenthal
2001 Genome Biology  
We found that in one member of this family, the human SPIN gene, each repeat resides in its own exon, supporting our view that Spin/Ssty repeats are independent functional units.  ...  Here we report the discovery of a new protein motif of around 50 amino acids in length, the Spin/Ssty repeat, in proteins of the Spin/Ssty (spindlin) family.  ...  The Spin/Ssty repeat alignment will assist in detecting further family members in other species and in the search for an evolutionary origin of the spindlin family of proteins.  ... 
pmid:11806826 pmcid:PMC150450 fatcat:ytpkalwbw5fgji7yp5g5eqg67q

Considering Transposable Element Diversification in De Novo Annotation Approaches

Timothée Flutre, Elodie Duprat, Catherine Feuillet, Hadi Quesneville, Ying Xu
2011 PLoS ONE  
Most begin with the detection of genomic repeats, but the subsequent steps for defining TE families differ.  ...  Several methods have been proposed for the de novo identification of TEs in sequenced genomes.  ...  This resulted in a list of pairwise alignments corresponding to repeats in the D. melanogaster and A. thaliana genome sequences.  ... 
doi:10.1371/journal.pone.0016526 pmid:21304975 pmcid:PMC3031573 fatcat:6v7yleiqpbgj5gm2cnjf5go4ia

ISQuest: finding insertion sequences in prokaryotic sequence fragment data

Abhishek Biswas, David T. Gauthier, Desh Ranjan, Mohammad Zubair
2015 Bioinformatics  
We tested ISQuest on simulated read libraries of 3810 complete bacterial genomes and plasmids in GenBank and were capable of detecting 82% of the ISs and transposases annotated in GenBank with 80% sequence  ...  This software identifies bacterial ISs and their sequence elements-inverted and direct repeats-in raw read data or contigs using flexible search parameters.  ...  Conflict of Interest: The work in this paper is supported by the Jeffress Trust Awards Program in Interdisciplinary Research and the M&S fellowship fund of the Old Dominion University.  ... 
doi:10.1093/bioinformatics/btv388 pmid:26116929 fatcat:ic3jddtmlzfjdcyma33ljboniy

Genome-Wide Analysis of Repeat Diversity across the Family Musaceae

Petr Novák, Eva Hřibová, Pavel Neumann, Andrea Koblížková, Jaroslav Doležel, Jiří Macas, Andreas Houben
2014 PLoS ONE  
However, there were quantitative differences and sequence variations detected for classified repeat families as well as for the bulk of total repetitive DNA.  ...  that will be instrumental in repeat masking and annotation in future genome assembly projects.  ...  Ines van den Houwe (ITC, Leuven) and Dr. François Côte (CIRAD, Guadeloupe) for providing the plant material and Dr. Nils Stein, Susanne König (IPK, Gatersleben), and Dr.  ... 
doi:10.1371/journal.pone.0098918 pmid:24932725 pmcid:PMC4059648 fatcat:vo2iixqrubdftoivok7vezoylu

Two novel PRP31 premessenger ribonucleic acid processing factor 31 homolog mutations including a complex insertion-deletion identified in Chinese families with retinitis pigmentosa

Bing Dong, Jieqiong Chen, Xiaohui Zhang, Zhe Pan, Fengge Bai, Yang Li
2013 Molecular Vision  
The deletion cosegregated with the family's disease phenotype, but was not found in 100 normal controls. No disease-causing mutation was detected in family RP24 with PCR-based sequencing analysis.  ...  Our results further confirmed that haploinsufficiency is the main mechanism for RP11 and that genomic arrangements may be prevalent in PRPF31 mutations.  ...  ACKNOWLEDGMENTS We thank the patients and their families for participating in this study. The study was supported by National Natural Science Foundation of China (No. 81170878).  ... 
pmid:24319336 pmcid:PMC3850970 fatcat:hea6ymvyojb2hd7klvyu62thou

Sequence Divergence Within Transposable Element Families in the Drosophila melanogaster Genome

E. Lerat
2003 Genome Research  
The publication costs of this article were defrayed in part by payment of page charges.  ...  This article must therefore be hereby marked "advertisement" in accordance with 18 USC section 1734 solely to indicate this fact.  ...  The tirant and zam Families No full-length copy of the zam element, of which only one copy was found in the genome (Rizzon et al. 2002) , was detected on the chromosome arms of the sequenced genome.  ... 
doi:10.1101/gr.827603 pmid:12869581 pmcid:PMC403780 fatcat:2pzweaxbabhhvjvgsygc3g35va

Alpha-CENTAURI: assessing novel centromeric repeat sequence variation with long read sequencing

Volkan Sevim, Ali Bashir, Chen-Shan Chin, Karen H. Miga
2016 Bioinformatics  
families in genomes without highquality reference assemblies.  ...  These sequences present a source of repeat structure diversity that is commonly ignored by standard genomic tools.  ...  repeat unit for a given satellite family.  ... 
doi:10.1093/bioinformatics/btw101 pmid:27153570 pmcid:PMC4920115 fatcat:ijs57gwxpfdslczs7o5dl4azgy

Draft Genome Sequence of Advenella kashmirensis Strain W13003, a Polycyclic Aromatic Hydrocarbon-Degrading Bacterium

X. Wang, D. Jin, L. Zhou, L. Wu, W. An, L. Zhao
2014 Genome Announcements  
Here, we report the 4.8-Mb draft genome sequence of this strain, which will provide insights into the diversity of A. kashmirensis and the mechanism of PAH degradation in the marine environment.  ...  Eighty-nine tandem repeats were detected, as revealed by Tandem Repeats Finder version 4.07 (12) . Only one incomplete prophage region was detected using PHAST (13) .  ...  The IS3 and IS21 families dominate the insertion sequence (IS) elements, as revealed by IS-Finder (14) .  ... 
doi:10.1128/genomea.00003-14 pmid:24482505 pmcid:PMC3907720 fatcat:fpe4p6igy5b7lingnuu2jzvx4y

DIRS and Ngaro Retrotransposons in Fungi

Anna Muszewska, Kamil Steczkiewicz, Krzysztof Ginalski, Nicolas Corradi
2013 PLoS ONE  
Yet, most of analyzed genomes are devoid of YR elements and most identified retrotransposons are incomplete.  ...  Interestingly, a single remnant Ngaro element could be identified in an Ascomycota genome.  ...  without or with incomplete repeats but still carrying at least a fragment of the aforementioned protein domains (genomic coordinates for all identified YR retroelements are provided in File S2).  ... 
doi:10.1371/journal.pone.0076319 pmid:24086727 pmcid:PMC3783388 fatcat:elgqb2vc4ffe7j7nicazcmfn7q
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