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WindowMasker: window-based masker for sequenced genomes

A. Morgulis, E. M. Gertz, A. A. Schaffer, R. Agarwala
2005 Bioinformatics  
, that may not exist for newly sequenced genomes.  ...  Results: We have developed a software tool called WindowMasker (WM) that identifies and masks highly repetitive DNA sequences in a genome, using only the sequence of the genome itself.  ...  We thank Victor Sapojnikov for assistance in testing both RM and WM and for guidance in enhancing the input/ output options so that WM could be used in NCBI's genome pipeline.  ... 
doi:10.1093/bioinformatics/bti774 pmid:16287941 fatcat:xsv5xz5zezeb5eu3uxdpecni3e

Red: an intelligent, rapid, accurate tool for detecting repeats de-novo on the genomic scale

Hani Z. Girgis
2015 BMC Bioinformatics  
With rapid advancements in technology, the sequences of thousands of species' genomes are becoming available. Within the sequences are repeats that comprise significant portions of genomes.  ...  As species-specific elements, repeats in newly sequenced genomes are likely to be unknown. Therefore, annotating newly sequenced genomes requires tools to discover repeats de-novo.  ...  Many thanks to Virginia LoCastro for her invaluable comments on my writing of this manuscript. The author wishes to thank David Landsman, Alex Astashyn, and David Managadze for useful discussions.  ... 
doi:10.1186/s12859-015-0654-5 pmid:26206263 pmcid:PMC4513396 fatcat:6zzd7olapfgwvin72vxon7allu

A novel genome-scale repeat finder geared towards transposons

Xuehui Li, Tamer Kahveci, A. Mark Settles
2007 Computer applications in the biosciences : CABIOS  
Our experiments on the Arabidopsis and rice genomes show that Greedier identifies approximately twice as many transposon bases as those found by cross_match and WindowMasker.  ...  Moreover, Greedier masks far fewer false positive bases than either cross_match or WindowMasker. In addition to masking repeats, Greedier also reports potential nested transposon structures.  ...  WindowMasker (ftp://ftp.ncbi.nih.gov/pub/agarwala/window masker/) is a de novo repeat finder that was developed specifically to mask large sequence databases.  ... 
doi:10.1093/bioinformatics/btm613 pmid:18089620 fatcat:nhgididz3vfybenjrhev5oav7y

Comparative Analysis of Teleost Genome Sequences Reveals an Ancient Intron Size Expansion in the Zebrafish Lineage

Stephen P. Moss, Domino A. Joyce, Stuart Humphries, Katherine J. Tindall, David H. Lunt
2011 Genome Biology and Evolution  
We have developed a bioinformatics pipeline for the comparative evolutionary analysis of Ensembl genomes and have used it to analyze the introns of the five available teleost fish genomes.  ...  We show our pipeline to be a powerful tool for revealing variation between genomes that may otherwise be overlooked with simple summary statistics.  ...  Casey Bergman, who advised on repeat sequence analysis; and to Dr. Andrew Davidson for providing input on the draft manuscript.  ... 
doi:10.1093/gbe/evr090 pmid:21920901 pmcid:PMC3205604 fatcat:brwrt4ppxvggxl746tyv2odpza

BLAST+: architecture and applications

Christiam Camacho, George Coulouris, Vahram Avagyan, Ning Ma, Jason Papadopoulos, Kevin Bealer, Thomas L Madden
2009 BMC Bioinformatics  
For long database sequences, it is possible to retrieve only the relevant parts of the sequence, reducing CPU time and memory usage for searches of short queries against databases of contigs or chromosomes  ...  Long query sequences are broken into chunks for processing, in some cases leading to dramatically shorter run times.  ...  Funding to pay the Open Access publication charges for this article was provided by the National Institutes of Health.  ... 
doi:10.1186/1471-2105-10-421 pmid:20003500 pmcid:PMC2803857 fatcat:qhqpojpbuvh4zffs4dvqs4beyi

Recombination landscape dimorphism contributes to sex chromosome evolution in the dioecious plant Rumex hastatulus [article]

Joanna L Rifkin, Solomiya Hnatovzka, Meng Yuan, Bianca M Sacchi, Baharul I Choudhury, Yunchen Gong, Pasi Rastas, Spencer C H Barrett, Stephen I Wright
2021 bioRxiv   pre-print
There is growing evidence across diverse taxa for sex differences in the genomic landscape of recombination, but the causes and consequences of these differences remain poorly understood.  ...  We provide evidence for strong sex differences in recombination, with pericentromeric regions of highly suppressed recombination in males that cover over half of the genome.  ...  Morgulis A, Gertz EM, Schäffer AA, Agarwala R. 2006 WindowMasker: window-based masker for Acknowledgments sequenced genomes. Bioinformatics 22, 134-141. 543 627 628 31.  ... 
doi:10.1101/2021.11.03.466946 fatcat:ckwdhs4mzzddzm76cf4poeruga

The draft chromosome-level genome assembly of tetraploid ground cherry (Prunus fruticosa Pall.) from long reads [article]

Thomas W Woehner, Ofere Francis Emeriewen, Alexander Wittenberg, Harrie Schneiders, Ilse Vrijenhoek, Julia Halasz, Karoly Hrotko, Katharina J. Hoff, Lars Gabriel, Jens Keilwagen, Thomas Berner, Mirko Schuster (+4 others)
2021 bioRxiv   pre-print
Using a homology and reference based scaffolding method, we generated a final consensus genome sequence of 366 Mb comprising eight chromosomes.  ...  BUSCO estimated a completeness between 98.7 % for the 4n and 96.1 % for the 1n datasets.  ...  WindowMasker: window-based 463 masker for sequenced genomes. Bioinformatics. 2006;22:134-41. 464 40. Lyons EH.  ... 
doi:10.1101/2021.06.01.446499 fatcat:yhdjrx52vzfkved7bptuphhhg4

Reconsidering the significance of genomic word frequencies

Miklós Csűrös, Laurent Noé, Gregory Kucherov
2007 Trends in Genetics  
Mitzenmacher, M. (2004) Dynamic models for file sizes and double Pareto distributions. 16 Internet Mathematics, 1:303-333. 17 [12] Morgulis, A. et al. (2006) WindowMasker: window-based masker for sequenced  ...  W. et al. (2006) Alignment statistics for long-range correlated genomic 15 sequences.  ...  Other sequences were downloaded from the NCBI FTP server (ftp://ftp.ncbi.nlm.nih.gov/genomes/).  ... 
doi:10.1016/j.tig.2007.07.008 pmid:17964682 fatcat:j5dmyg3xqbbnvh44jtzbksrki4

NCBI BLAST+ integrated into Galaxy [article]

Peter J. A. Cock, John M. Chilton, Björn Grüning, James E. Johnson, Nicola Soranzo
2015 bioRxiv   pre-print
For early adopters of the Galaxy web-based biomedical data analysis platform, integrating BLAST was a natural step for sequence comparison workflows.  ...  The NCBI BLAST suite has become ubiquitous in modern molecular biology, used for small tasks like checking capillary sequencing results of single PCR products through to genome annotation or even larger  ...  Acknowledgements We thank NCBI BLAST team for their long running work, the Galaxy Team for their assistance and advice, the Galaxy Community for their feedback and suggestions, and the past, present and  ... 
doi:10.1101/014043 fatcat:m25asfzatrf4lmfxi233t4zwye

Calling SNPs without a reference sequence

Aakrosh Ratan, Yu Zhang, Vanessa M Hayes, Stephan C Schuster, Webb Miller
2010 BMC Bioinformatics  
The most common application for the next-generation sequencing technologies is resequencing, where short reads from the genome of an individual are aligned to a reference genome sequence for the same species  ...  Conclusions: DIAL can be used for identification of nucleotide differences in species for which no reference sequence is available.  ...  Acknowledgements We thank Devin Locke and the Orangutan Consortium for giving us access to the orangutan sequence data.  ... 
doi:10.1186/1471-2105-11-130 pmid:20230626 pmcid:PMC2851604 fatcat:wcceed4annbwdjkxxff6sks6rq

RepeatFiller newly identifies megabases of aligning repetitive sequences and improves annotations of conserved non-exonic elements [article]

Ekaterina Osipova, Nikolai Hecker, Michael Hiller
2019 bioRxiv   pre-print
Repetitive sequences can be co-opted into a variety of functions and thus provide a source for evolutionary novelty.  ...  Transposons and other repetitive sequences make up a large part of complex genomes.  ...  Acknowledgment We thank the genomics community for sequencing and assembling the genomes and the UCSC genome browser group for providing software and genome annotations.  ... 
doi:10.1101/696922 fatcat:wdq65vi2bvdu3jejsa4z7yykza

Chromosomal-Level Assembly of the Asian Seabass Genome Using Long Sequence Reads and Multi-layered Scaffolding

Shubha Vij, Heiner Kuhl, Inna S. Kuznetsova, Aleksey Komissarov, Andrey A. Yurchenko, Peter Van Heusden, Siddharth Singh, Natascha M. Thevasagayam, Sai Rama Sridatta Prakki, Kathiresan Purushothaman, Jolly M. Saju, Junhui Jiang (+37 others)
2016 PLoS Genetics  
size over 1 Mb and scaffold N50 size over 25 Mb that span~90% of the genome.  ...  We report here the~670 Mb genome assembly of the Asian seabass (Lates calcarifer), a tropical marine teleost.  ...  Acknowledgments We thank Campbell Rae and Thoba Lose at the South African National Bioinformatics Institute for designing the seabass genome web portal and the genome explorer, Vydianathan Ravi for helping  ... 
doi:10.1371/journal.pgen.1005954 pmid:27082250 pmcid:PMC4833346 fatcat:pxthwcc56bcwrolilscc7gcjt4

The Egyptian Rousette Genome Reveals Unexpected Features of Bat Antiviral Immunity

Stephanie S. Pavlovich, Sean P. Lovett, Galina Koroleva, Jonathan C. Guito, Catherine E. Arnold, Elyse R. Nagle, Kirsten Kulcsar, Albert Lee, Françoise Thibaud-Nissen, Adam J. Hume, Elke Mühlberger, Luke S. Uebelhoer (+5 others)
2018 Cell  
To identify differences between antiviral mechanisms in humans and bats, we sequenced, assembled, and analyzed the genome of Rousettus aegyptiacus, a natural reservoir of Marburg virus and the only known  ...  reservoir for any filovirus.  ...  Window-Masker: window-based masker for sequenced genomes. Bioinformatics 22, 134-141. Mudunuri, U., Che, A., Yi, M., and Stephens, R.M. (2009). bioDBnet: the biological database network.  ... 
doi:10.1016/j.cell.2018.03.070 pmid:29706541 pmcid:PMC7112298 fatcat:e4nfrn3torbvdbnjukjh6wpm2q

Towards complete and error-free genome assemblies of all vertebrate species

Arang Rhie, Shane A McCarthy, Olivier Fedrigo, Joana Damas, Giulio Formenti, Sergey Koren, Marcela Uliano-Silva, William Chow, Arkarachai Fungtammasan, Juwan Kim, Chul Lee, Byung June Ko (+115 others)
2021 Nature  
We confirm that long-read sequencing technologies are essential for maximizing genome quality, and that unresolved complex repeats and haplotype heterozygosity are major sources of assembly error when  ...  Our assemblies correct substantial errors, add missing sequence in some of the best historical reference genomes, and reveal biological discoveries.  ...  WindowMasker: window-based Program of the NHGRI, NIH (1ZIAHG200398). A.R. was also supported by the Korea Health masker for sequenced genomes.  ... 
doi:10.1038/s41586-021-03451-0 pmid:33911273 pmcid:PMC8081667 fatcat:xpk4xiuthfb7hf5wmxaavhfpbu

A modifier of Huntington's disease onset at the MLH1 locus

Jong-Min Lee, Michael J. Chao, Denise Harold, Kawther Abu Elneel, Tammy Gillis, Peter Holmans, Lesley Jones, Michael Orth, Richard H. Myers, Seung Kwak, Vanessa C. Wheeler, Marcy E. MacDonald (+1 others)
2017 Human Molecular Genetics  
A recent genome-wide association analysis to discover genetic modifiers of HD onset age provided initial evidence for modifier loci on chromosomes 8 and 15 and suggestive evidence for a locus on chromosome  ...  Genomic DNA capture and sequencing of a modifier haplotype localize the functional variation to a 78 kb region spanning the 3'end of MLH1 and the 5'end of the neighboring LRRFIP2, and marked by an isoleucine-valine  ...  Morgulis, A., Gertz, E.M., Schaffer, A.A. and Agarwala, R. (2006) WindowMasker: window-based masker for sequenced genomes. Bioinformatics, 22, 134-141. 35.  ... 
doi:10.1093/hmg/ddx286 pmid:28934397 pmcid:PMC6455020 fatcat:hlwsbodtdzdnzdfaf5qykslfna