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Designing Efficient Spaced Seeds for SOLiD Read Mapping

Laurent Noé, Marta Gîrdea, Gregory Kucherov
2010 Advances in Bioinformatics  
SOLiD color-space reads to a reference genome.  ...  We illustrate our approach by several seed designs and demonstrate their efficiency.  ...  They also thank Martin Figeac (Institut national de la santé et de la recherche médicale) for sharing insightful knowledge about the SOLiD technology. L.  ... 
doi:10.1155/2010/708501 pmid:20936175 pmcid:PMC2945724 fatcat:nahdomgtm5bfpf3pk2mrmifh2i

PerM: efficient mapping of short sequencing reads with periodic full sensitive spaced seeds

Yangho Chen, Tade Souaiaia, Ting Chen
2009 Computer applications in the biosciences : CABIOS  
Results: We present the mapping software, named PerM (Periodic Seed Mapping) that uses periodic spaced seeds to significantly improve mapping efficiency for large reference genomes when compared to state-of-the-art  ...  Such sensitivity makes PerM a valuable mapping tool for SOLiD and Solexa reads.  ...  Andrew Smith at USC for providing us with data and helpful suggestions.  ... 
doi:10.1093/bioinformatics/btp486 pmid:19675096 pmcid:PMC2752623 fatcat:rhgu7qtoijazhd57r5q5ysipvi

Seed Design Framework for Mapping SOLiD Reads [chapter]

Laurent Noé, Marta Gîrdea, Gregory Kucherov
2010 Lecture Notes in Computer Science  
We propose a rigorous and flexible algorithmic solution to mapping SOLiD color-space reads to a reference genome.  ...  We illustrate our approach by several seed designs and demonstrate their efficiency.  ...  We also thank Martin Figeac (Institut national de la santé et de la recherche médicale) for sharing insightful knowledge about the SOLiD technology.  ... 
doi:10.1007/978-3-642-12683-3_25 fatcat:65fdkd7yjrgkrpcoujaeqjlw7y

ZOOM Lite: next-generation sequencing data mapping and visualization software

Z. Zhang, H. Lin, B. Ma
2010 Nucleic Acids Research  
In this article, we present ZOOM Lite, a software for efficient reads mapping and result visualization.  ...  With a kernel capable of mapping tens of millions of Illumina or AB SOLiD sequencing reads efficiently and accurately, and an intuitive graphical user interface, ZOOM Lite integrates reads mapping and  ...  We also want to thank Wes Farquharson for the effort to polish the English writing. Conflict of interest statement. None declared.  ... 
doi:10.1093/nar/gkq538 pmid:20530531 pmcid:PMC2896157 fatcat:qhdobau5unhxhb3hgnzpbsn7ke

ZOOM! Zillions of oligos mapped

H. Lin, Z. Zhang, M. Q. Zhang, B. Ma, M. Li
2008 Bioinformatics  
Results: We present a framework for how full sensitivity mapping can be done in the most efficient way, via spaced seeds.  ...  Resequencing and personalized medicine need much faster software to map these deep sequencing reads to a reference genome, to identify SNPs or rare transcripts.  ...  Andrew Smith for providing the RMAP software and many valuable suggestions, Dr Zhenyu Xuan for the experimental BAC data before publication, Aaron Quinlan and Michael Stromberg for the Mosaik beta version  ... 
doi:10.1093/bioinformatics/btn416 pmid:18684737 pmcid:PMC2732274 fatcat:5xloilck6nf7tc7izg3rwsr4ja

Evaluation of next-generation sequencing software in mapping and assembly

SuYing Bao, Rui Jiang, WingKeung Kwan, BinBin Wang, Xu Ma, You-Qiang Song
2011 Journal of Human Genetics  
However, reads from next-generation sequencing (NGS) platforms, such as 454/Roche, ABI/SOLiD and Illumina/Solexa, are usually short, thereby restricting the applications of NGS platforms in genome assembly  ...  We presented an overview of the challenges that these novel technologies meet and particularly illustrated various bioinformatics attempts on mapping and assembly for problem solving.  ...  CloudBurst, presented by Schatz et al., 15 is a sensitive parallel seed-and-extend read-mapping algorithm, optimized for mapping single-end (SE) reads.  ... 
doi:10.1038/jhg.2011.62 pmid:21677664 fatcat:7v3jia5x4rgvrmfzjm5dgncdsy

A survey of sequence alignment algorithms for next-generation sequencing

H. Li, N. Homer
2010 Briefings in Bioinformatics  
We come to the conclusion that short-read alignment is no longer the bottleneck of data analyses.  ...  A central challenge to the analysis of this data is sequence alignment, whereby sequence reads must be compared to a reference.  ...  Many other aligners [26] [27] [28] also use spaced seed with different templates designed specifically for the reference genome and sensitivity tolerances, making spaced seed the most popular approach  ... 
doi:10.1093/bib/bbq015 pmid:20460430 pmcid:PMC2943993 fatcat:p2qoot222zblhgylxjtmaihu54

Evaluation of next-generation sequencing software in mapping and assembly

Suying Bao, Rui Jiang, WingKeung Kwan, BinBin Wang, Xu Ma, You-Qiang Song
2011 Journal of Human Genetics  
However, reads from next-generation sequencing (NGS) platforms, such as 454/Roche, ABI/SOLiD and Illumina/Solexa, are usually short, thereby restricting the applications of NGS platforms in genome assembly  ...  We presented an overview of the challenges that these novel technologies meet and particularly illustrated various bioinformatics attempts on mapping and assembly for problem solving.  ...  Algorithms involved with advanced spaced seeds would be a considerable modification for SOLiD mappers, as in Laurent Noe et al. 36 As this review mainly focuses on comparing the capacities of Illumina  ... 
doi:10.1038/jhg.2011.43 pmid:21525877 fatcat:ontauwv5kze2jnp6pmmjkazgca

BatMeth: improved mapper for bisulfite sequencing reads on DNA methylation

Jing-Quan Lim, Chandana Tennakoon, Guoliang Li, Eleanor Wong, Yijun Ruan, Chia-Lin Wei, Wing-Kin Sung
2012 Genome Biology  
However, bisulfite conversion introduces mismatches between the reads and the reference genome, which makes mapping of Illumina and SOLiD reads slow and inaccurate.  ...  BatMeth is an algorithm that integrates novel Mismatch Counting, List Filtering, Mismatch Stage Filtering and Fast Mapping onto Two Indexes components to improve unique mapping rate, speed and precision  ...  Figure 4b outlines the algorithm and shows how the components are assembled for SOLiD color-space bisulfite read mapping.  ... 
doi:10.1186/gb-2012-13-10-r82 pmid:23034162 pmcid:PMC3491410 fatcat:vqtj5ngatfetjcb22im36k6dc4

SHRiMP: Accurate Mapping of Short Color-space Reads

Stephen M. Rumble, Phil Lacroute, Adrian V. Dalca, Marc Fiume, Arend Sidow, Michael Brudno, Wyeth W. Wasserman
2009 PLoS Computational Biology  
Our method is based upon a fast read mapping technique, separate thorough alignment methods for regular letter-space as well as AB SOLiD (color-space) reads, and a statistical model for false positive  ...  Citation: Rumble SM, Lacroute P, Dalca AV, Fiume M, Sidow A, et al. (2009) SHRiMP: Accurate Mapping of Short Color-space Reads. PLoS Comput Biol 5(5): e1000386.  ...  Acknowledgments We thank Ziming Weng for preparing the C. savignyi library and Cheryl Smith for sequencing the library. We also thank Aston Wallis for proofing the manuscript. Author Contributions  ... 
doi:10.1371/journal.pcbi.1000386 pmid:19461883 pmcid:PMC2678294 fatcat:xi2byt525vdxbbyr7dwk3phrpu

Mapping and differential expression analysis from short-read RNA-Seq data in model organisms

Qiong-Yi Zhao, Jacob Gratten, Restuadi Restuadi, Xuan Li
2016 Quantitative Biology  
For model organisms with a reference genome, the first step in analysis of RNA-Seq data involves mapping of short-read sequences to the reference genome.  ...  Following read mapping, the primary interest of biologists in many RNA-Seq studies is the investigation of differential expression between experimental groups.  ...  Jennifer Whitehead for critical reading of the manuscript. This work is supported by the National Health and Medical Research Council project grants (Nos.  ... 
doi:10.1007/s40484-016-0060-7 fatcat:idomdo4pdjgr3o7jvz44w2uxlu

Flash memory efficient LTL model checking

S. Edelkamp, D. Sulewski, J. Barnat, L. Brim, P. Šimeček
2011 Science of Computer Programming  
For flash memory efficient off-line LTL model checking, which aims at generating a minimal counterexample and scans the entire state space at least once, we analyze the effect of outsourcing a memory-based  ...  Currently, most solid-state disks are based on NAND technology and much faster than magnetic disks in random reads, while in random writes they are generally not.  ...  Acknowledgements We would like to thank Martin Dietzfelbinger for his help to derive the lower bound on perfect hashing, Peter Kissmann for his rigorous proof reading, and the anonymous reviewers for the  ... 
doi:10.1016/j.scico.2010.03.005 fatcat:5kkssybrs5dibhqgwyhvsv3xfi

Fast and accurate mapping of Complete Genomics reads

Donghyuk Lee, Farhad Hormozdiari, Hongyi Xin, Faraz Hach, Onur Mutlu, Can Alkan
2015 Methods  
Here we provide a sensitive read mapper (sirFAST) for the CG technology based on the seed-and-extend paradigm that can quickly map CG reads to a reference genome.  ...  The first problem to tackle in analyzing HTS data for resequencing applications is the read mapping stage, where many tools have been developed for the most popular HTS methods, but publicly available  ...  We designed sirFAST to efficiently align such reads to the reference assembly, at the presence of the flexible ''expected'' gaps/overlaps within each read.  ... 
doi:10.1016/j.ymeth.2014.10.012 pmid:25461772 pmcid:PMC4406782 fatcat:qkbmuxfcq5dgrl4iongu6c7qd4

Novel Computational Techniques For Mapping And Classifying Next-Generation Sequencing Data

Karel Břinda, Gregory Kucherov, Valentina Boeva
2016 Zenodo  
In this thesis, we present novel computational techniques for read mapping and taxonomic classification. With more than a hundred of published mappers, read mapping might be considered fully solved.  ...  Dynamic mapping is based on exploiting the information from previously computed alignments, helping to improve the mapping of subsequent reads.  ...  Designing efficient seeds for metagenomic classification is another important issue that goes beyond the present study.  ... 
doi:10.5281/zenodo.1045317 fatcat:agbwpocisncwvihn2ij5q3ongq

Genome variation discovery with high-throughput sequencing data

A. V. Dalca, M. Brudno
2010 Briefings in Bioinformatics  
In this paper, we overview HTS technologies and discuss several of the plethora of algorithms and tools designed to analyze HTS data, including algorithms for read mapping, as well as methods for identification  ...  of single-nucleotide polymorphisms, insertions/deletions and large-scale structural variants and copy-number variants from these mappings.  ...  Figure 2 : 2 Methods for fast read matching. The multiple spaced seeds approach as utilized in Zoom (A).  ... 
doi:10.1093/bib/bbp058 pmid:20053733 fatcat:rmhcyfmaovchnndc7a7b3durni
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