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An Approximate de Bruijn Graph Approach to Multiple Local Alignment and Motif Discovery in Protein Sequences [chapter]

Rupali Patwardhan, Haixu Tang, Sun Kim, Mehmet Dalkilic
2006 Lecture Notes in Computer Science  
We generalize their approach to aligning protein sequences by building an approximate de Bruijn graph to allow gluing similar but not identical amino acids.  ...  We introduce a new algorithm for multiple local alignment for protein sequences, based on the de Bruijn graph approach first proposed by Zhang and Waterman for aligning DNA sequence.  ...  We thank members of the Bioinformatics Research Group at the School of Informatics, and the members of the Bioinformatics Team at Center for Genomics and Bioinformatics for many helpful discussions.  ... 
doi:10.1007/11960669_14 fatcat:7aqud6hkfnezhnz4k4yd6jtzle

Accurate de novo and transmitted indel detection in exome-capture data using microassembly

Giuseppe Narzisi, Jason A O'Rawe, Ivan Iossifov, Han Fang, Yoon-ha Lee, Zihua Wang, Yiyang Wu, Gholson J Lyon, Michael Wigler, Michael C Schatz
2014 Nature Methods  
The authors declare no competing financial interests. reprints and permissions information is available online at http://www.nature. com/reprints/index.html.  ...  Graph traversal. Once a valid de Bruijn graph is constructed, Scalpel examines the graph to find end-to-end sequence paths that span the target window.  ...  Reads aligning to the region are extracted and decomposed into overlapping k-mers. In order to model the double-stranded nature of the DNA, a bidirected de Bruijn graph is constructed 31, 32 .  ... 
doi:10.1038/nmeth.3069 pmid:25128977 pmcid:PMC4180789 fatcat:eunwoeus3beu5bq33ianeyilii

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  ...  Acknowledgements We thank Thomas Bureau, Douglas Hoen and Nikoleta Juretic for helpful discussions and two anonymous reviewers for helpful comments on the manuscript.  ... 
doi:10.1093/bib/bbm048 pmid:17932080 fatcat:r2cjoizumbczjbwe2oosm6irpi

The parallelism motifs of genomic data analysis

Katherine Yelick, Aydın Buluç, Muaaz Awan, Ariful Azad, Benjamin Brock, Rob Egan, Saliya Ekanayake, Marquita Ellis, Evangelos Georganas, Giulia Guidi, Steven Hofmeyr, Oguz Selvitopi (+2 others)
2020 Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences  
Genomic datasets are growing dramatically as the cost of sequencing continues to decline and small sequencing devices become available.  ...  We consider several problems in high-performance genomics analysis, including alignment, profiling, clustering and assembly for both single genomes and metagenomes.  ...  Once the contigs are formed, the assembler builds a graph with contig vertices and uses alignment to find reads that align to multiple contigs and thus form an edge in the contig graph.  ... 
doi:10.1098/rsta.2019.0394 pmid:31955674 fatcat:kzujmq5u2refvhoovtb2ap5vha

A compact, in vivo screen of all 6-mers reveals drivers of tissue-specific expression and guides synthetic regulatory element design

Robin P Smith, Samantha J Riesenfeld, Alisha K Holloway, Qiang Li, Karl K Murphy, Natalie M Feliciano, Lorenzo Orecchia, Nir Oksenberg, Katherine S Pollard, Nadav Ahituv
2013 Genome Biology  
To enable this large-scale screen, we developed algorithms that use a reverse-complement aware decomposition of the de Bruijn graph to design a library of DNA oligomers incorporating every 6-bp sequence  ...  To enable this large-scale screen, we developed algorithms that use a reverse-complement aware decomposition of the de Bruijn graph to design a library of DNA oligomers incorporating every 6-bp sequence  ...  SJR is supported by a PhRMA Foundation Post Doctoral Fellowship in Bioinformatics, NICHD NRSA number 1F32HD069168, and a gift to the Pollard lab from the San Simeon Fund.  ... 
doi:10.1186/gb-2013-14-7-r72 pmid:23867016 pmcid:PMC4054837 fatcat:vdn5rklsyrdvlbmzzcjuhtbwyy

Computational Approaches and Tools Used in Identification of Dispersed Repetitive DNA Sequences

Surya Saha, Susan Bridges, Zenaida V. Magbanua, Daniel G. Peterson
2008 Tropical Plant Biology  
It has become clear that dispersed repeat sequences have played multiple roles in eukaryotic genome evolution including increasing genetic diversity through mutation, inducing changes in gene expression  ...  We conclude by discussing the strengths and weaknesses of current tools and highlighting additional approaches that may advance repeat discovery/characterization.  ...  The focus is on deciphering the mosaic of sub-repeats nested within repetitive regions in the genome using A-Bruijn graphs, an extension of the de Bruijn graphs [22] .  ... 
doi:10.1007/s12042-007-9007-5 fatcat:uswrzc4cijdm5i4su4vra4qsyi

Joint Alignment of Multiple Protein–Protein Interaction Networks via Convex Optimization

Somaye Hashemifar, Qixing Huang, Jinbo Xu
2016 Journal of Computational Biology  
HSA is robust, accurate, and outperforms or rivals existing computational tools when evaluated on simulated and real datasets in diverse cell types.  ...  However, few computational approaches are existing to quantitatively analyze Hi-C data, thus hindering the investigation of the association between 3D chromatin structure and genome function.  ...  This is a misunderstanding since the de Bruijn approach, as well as its variation called the A-Bruijn graph approach [2] , was originally developed to assemble rather long Sanger reads.  ... 
doi:10.1089/cmb.2016.0025 pmid:27428933 fatcat:tr4e3u3hqjaoziavhhsklxkkmi

Genetic variation and the de novo assembly of human genomes

Mark J. P. Chaisson, Richard K. Wilson, Evan E. Eichler
2015 Nature reviews genetics  
The discovery of genetic variation and the assembly of genome sequences are both inextricably linked to advances in DNA-sequencing technology.  ...  Here, we review approaches to genome assembly, the nature of gaps or missing sequences, and biases in the assembly process.  ...  Brown for assistance in editing this manuscript. This work was supported, in part, by a US National Institutes of Health grant (2R01HG002385) to E.E.E..  ... 
doi:10.1038/nrg3933 pmid:26442640 pmcid:PMC4745987 fatcat:ukhbax4w6rgqzdoz5ce25ysa44

Whole-Genome Alignment [chapter]

Colin N. Dewey
2019 Msphere  
It combines aspects of both colinear sequence alignment and gene orthology prediction and is typically more challenging to address than either of these tasks due to the size and complexity of whole genomes  ...  In this chapter, we discuss the meaning and significance of WGA and present an overview of the methods that address it.  ...  DRIMM-Synteny and OSfinder use A-Bruijn graphs and Sibelia uses de Bruijn graphs, of which A-Bruijn graphs are a generalization.  ... 
doi:10.1007/978-1-4939-9074-0_4 pmid:31278663 fatcat:clhkkvaq7vawpj3mtlkpaujicm

The Basics of Protein Sequence Analysis [chapter]

Katarzyna H. Kaminska, Kaja Milanowska, Janusz M. Bujnicki
2008 Prediction of Protein Structures, Functions, and Interactions  
Acknowledgements We thank present and former members of the Bujnicki lab in IIMCB and at the UAM for stimulating discussions and contribution of ideas and information to this article.  ...  KHK has worked on this article while being supported by a fellowship from EMBO and a travel grant from Polish Academy of Sciences and JSPS.  ...  Enables alignment of protein sequences with multiple domains AliWABA 128 aba.nbcr.net/ A-Bruijn Alignment represents an alignment as a directed graph, possibly containing cycles.  ... 
doi:10.1002/9780470741894.ch1 fatcat:5mafpeqhyjadlme2dmsl7weymq

Detection of simple and complex de novo mutations with multiple reference sequences

Kiran V. Garimella, Zamin Iqbal, Michael A. Krause, Susana Campino, Mihir Kekre, Eleanor Drury, Dominic Kwiatkowski, Juliana M. Sá, Thomas E. Wellems, Gil McVean
2020 Genome Research  
We construct multisample, colored de Bruijn graphs from short-read data for all samples, align long-read-derived haplotypes and multiple reference data sources to restore graph connectivity information  ...  The characterization of de novo mutations in regions of high sequence and structural diversity from whole-genome sequencing data remains highly challenging.  ...  Acknowledgments We thank Eric Antoniou, Sara Goodwin, Michael Schatz, Author contributions: K.V.G. developed algorithms and pipelines for identifying mutations in sequence assembly graphs.  ... 
doi:10.1101/gr.255505.119 pmid:32817236 pmcid:PMC7462078 fatcat:zonrqbfvtvdcleaxmgnci7uuay

Accurate detection of de novo and transmitted INDELs within exome-capture data using micro-assembly [article]

Giuseppe Narzisi, Jason A O'Rawe, Ivan Iossifov, Han Fang, Yoon-ha Lee, Zihua Wang, Yiyang Wu, Gholson J Lyon, Michael Wigler, Michael C Schatz
2013 bioRxiv   pre-print
By combining the power of mapping and assembly, Scalpel carefully searches the de Bruijn graph for sequence paths that span each exon.  ...  A detailed repeat analysis coupled with a self-tuning k-mer strategy allows Scalpel to outperform other state-of-the-art approaches for INDEL discovery.  ...  Cortex is a de-novo sequence assembler that uses colored de Bruijn graphs for detecting genetic variants.  ... 
doi:10.1101/001370 fatcat:fmda5qgcf5dinca2xpwxvy7pvu

De novo assembly and characterization of bark transcriptome using Illumina sequencing and development of EST-SSR markers in rubber tree (Hevea brasiliensis Muell. Arg.)

Dejun Li, Zhi Deng, Bi Qin, Xianghong Liu, Zhonghua Men
2012 BMC Genomics  
In total, 22,756 unigenes with an average length of 485 bp were obtained with de novo assembly.  ...  The similarity search indicated that 16,520 and 12,558 unigenes showed significant similarities to known proteins from NCBI non-redundant and Swissprot protein databases, respectively.  ...  In addition, he drafted and revised the manuscript. ZD and BQ participated in data analyses and SSR validation. XL conducted samples collection and preparation.  ... 
doi:10.1186/1471-2164-13-192 pmid:22607098 pmcid:PMC3431226 fatcat:zo5dv2dq3rfvpew63pm7fxd3nq

Identification of conserved splicing motifs in mutually exclusive exons of 15 insect species

Patricia Buendia, John Tyree, Robert Loredo, Shu-Ning Hsu
2012 BMC Genomics  
Our method, ESTs-to-ESRs (E2E), uses graph analysis of EST splicing graphs to identify mutually exclusive (ME) exons and combines phylogenetic measures, a sliding window approach along the multiple alignment  ...  Methods: In this paper, we describe an in silico analysis pipeline to extract putative exonic splicing regulatory sequences from a multiple alignment of 15 species of insects.  ...  Akira Chiba for his involvement in the initial phase of this project. We also thank Dr. Xin Wang's team for providing us with their list of regulatory elements.  ... 
doi:10.1186/1471-2164-13-s2-s1 pmid:22537296 pmcid:PMC3303723 fatcat:kcti2h7dpjbxvgxwhmchalas7q

Selected abstracts of "Bioinformatics: from Algorithms to Applications 2020" conference

2020 BMC Bioinformatics  
O5 A rigorous approach to pairwise distance analysis of a protein family via multi-dimensional scaling and its application to the genealogy of squalene synthase paralogues of green algae Acknowledgments  ...  P8 Installing and searching BLAST databases in a data science framework Graham Alvare 1 , Abiel Roche-Lima 2 , Brian Fristensky 3* Acknowledgments This research was supported by the Russian Science  ...  Indexing De Bruijn graphs with minimizers. In Recomb seq. 4 Marchet, C., Iqbal, Z., Gautheret, D., Salson, M. and Chikhi, R., 2020.  ... 
doi:10.1186/s12859-020-03838-2 pmid:33327929 fatcat:2t65jee32rgsnohhdwd7vbwj74
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