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Finding Anchors for Genomic Sequence Comparison

Ross A. Lippert, Xiaoyue Zhao, Liliana Florea, Clark Mobarry, Sorin Istrail
2005 Journal of Computational Biology  
FINDING ANCHORS FOR GENOMIC SEQUENCE COMPARISON 763 or point out assembly errors, and to ease annotation efforts by tracking of features such as genes, SNPs, and STS markers between different assembly  ...  A similar method for detecting genome rearrangements is described by Kent et al. (2003) . One daunting challenge to alignment programs is sequence repetitiveness.  ...  ACKNOWLEDGMENTS We thank Mike Waterman for fruitful discussions on the statistical modeling of exact matches.  ... 
doi:10.1089/cmb.2005.12.762 pmid:16108715 fatcat:w5d6m5cfpnha7pzackjl3zvq2m

Finding anchors for genomic sequence comparison

Ross A. Lippert, Xiaoyue Zhao, Liliana Florea, Clark Mobarry, Sorin Istrail
2004 Proceedings of the eighth annual international conference on Computational molecular biology - RECOMB '04  
two genomes can be found in selected exact matches, with very limited amount of sequence duplication.  ...  We present a statistical framework and practical methods for selecting a set of matches that is both sensitive and specific and can constitute a reliable set of anchors for a one-to-one mapping of two  ...  Table 7 : 7 Designing anchors for the comparison of NCBI 28 and NCBI 34. Table 8 : 8 Estimation of the variation of the Monte Carlo method.  ... 
doi:10.1145/974614.974645 dblp:conf/recomb/LippertZFMI04 fatcat:2ifa7ewrj5ei5cqkcazbvmihuu

ABWGAT: anchor-based whole genome analysis tool

Sarbashis Das, Anchal Vishnoi, Alok Bhattacharya
2009 Computer applications in the biosciences : CABIOS  
Here we present a simple web-based interface for whole genome comparison named ABWGAT (Anchor-Based Whole Genome Analysis Tool) that is simple to use.  ...  Large numbers of genomes are being sequenced regularly and the rate will go up in future due to availability of new genome sequencing techniques.  ...  ACKNOWLEDGEMENTS We thanks to CDAC (Center for Development of Advance Computing) for help in implementing parallel computing. Conflict of Interest: none declared.  ... 
doi:10.1093/bioinformatics/btp587 pmid:19828577 fatcat:owr2xhhqkrfglahkqn6yrmu3mi

Murasaki: A Fast, Parallelizable Algorithm to Find Anchors from Multiple Genomes

Kris Popendorf, Hachiya Tsuyoshi, Yasunori Osana, Yasubumi Sakakibara, Darren P. Martin
2010 PLoS ONE  
With the number of available genome sequences increasing rapidly, the magnitude of sequence data required for multiple-genome analyses is a challenging problem.  ...  sequence comparisons of multiple genomes quickly becomes a limiting factor as the number and scale of genomes grows.  ...  Mauve [4] , for example, relies on anchors only for finding the endpoints of alignable collinear regions.  ... 
doi:10.1371/journal.pone.0012651 pmid:20885980 pmcid:PMC2945767 fatcat:mxufo75awzayrch7bnxe2zznjq

An applications-focused review of comparative genomics tools: Capabilities, limitations and future challenges

P. Chain
2003 Briefings in Bioinformatics  
A review of some recent tools for multisequence/genome alignment and substring comparison is presented, within the general framework of applicability to a large-scale application.  ...  We note that genome alignments are important for many things, only one of which is pathogen detection.  ...  Thanks also to Burkhard Morgenstern for his suggestions improving the description of DIALIGN.  ... 
doi:10.1093/bib/4.2.105 pmid:12846393 fatcat:3p5ybliqe5earn3hz4bmatuljy

Mauve: Multiple Alignment of Conserved Genomic Sequence With Rearrangements

A. C.E. Darling
2004 Genome Research  
ACKNOWLEDGMENTS We thank Mark Craven for insightful comments and suggestions. Funding for this research was provided by NIH Grant GM62994-02.  ...  In addition to identifying local changes in the sequences of individual genes, the availability of genome sequences provides a basis for comparison of the structure and organization of genomes as a whole  ...  Although Shuffle-LAGAN's alignment approach works for pairwise comparison, an extension of the method to multiple genome sequences has not yet been suggested.  ... 
doi:10.1101/gr.2289704 pmid:15231754 pmcid:PMC442156 fatcat:bssse7intvavxc5chxshzlpufm

Pash: Efficient Genome-Scale Sequence Anchoring by Positional Hashing

K. J. Kalafus
2004 Genome Research  
Using modest computing resources, we employed Pash for two large-scale sequence comparison tasks: comparison of three mammalian genomes, and anchoring millions of chimpanzee whole-genome shotgun sequencing  ...  Pash is a computer program for efficient, parallel, all-against-all comparison of very long DNA sequences.  ...  ACKNOWLEDGMENTS We are grateful to the Baylor Human Genome Sequencing Center for use of computing resources; the Rat Genome Sequencing Consortium for providing valuable feedback; Manuel L.  ... 
doi:10.1101/gr.1963804 pmid:15060009 pmcid:PMC383312 fatcat:7xnxwzp6gjdknj4sio2vhv7dym

AVID: A Global Alignment Program

N. Bray
2002 Genome Research  
The method is designed to be fast, memory efficient, and practical for sequence alignments of large genomic regions up to megabases long.  ...  We present numerous applications of the method, ranging from the comparison of assemblies to alignment of large syntenic genomic regions and whole genome human/mouse alignments.  ...  Thanks also to the Mouse Sequencing Consortium for generating whole genome mouse sequence, which helped greatly in refining and streamlining AVID.  ... 
doi:10.1101/gr.789803 pmid:12529311 pmcid:PMC430967 fatcat:7gnoeoimpjf5foh5236haowj5q

SyMAP v3.4: a turnkey synteny system with application to plant genomes

Carol Soderlund, Matthew Bomhoff, William M. Nelson
2011 Nucleic Acids Research  
SyMAP (Synteny Mapping and Analysis Program) was originally developed to compute synteny blocks between a sequenced genome and a FPC map, and has been extended to support pairs of sequenced genomes.  ...  The software may be used from a website or standalone for the best performance. A project manager is provided to organize and automate the analysis of multi-genome groups.  ...  Anchor loading and synteny analysis The original SyMAP synteny algorithm (1) works without change for the comparison of sequenced genomes, since its input is the anchor coordinates from the two genomes  ... 
doi:10.1093/nar/gkr123 pmid:21398631 pmcid:PMC3105427 fatcat:h6mwrr26ivfdvbhyq56p7y23m4

Comparative analysis of bacterial genomes: identification of divergent regions in mycobacterial strains using an anchor-based approach

Anchal Vishnoi, Rahul Roy, Alok Bhattacharya
2007 Nucleic Acids Research  
ABWGC is based on random sampling of anchor sequences from one genome, followed by analysis of sampled and homologous regions from the target genome.  ...  In this report, we describe an anchorbased whole genome comparison (ABWGC) method.  ...  Bhattacharya and Vivek Thakur for discussion and valuable comments. The authors thank the anonymous referees for valuable suggestions.  ... 
doi:10.1093/nar/gkm209 pmid:17488849 pmcid:PMC1931498 fatcat:iusrd5b3bfhp7euvfhxbdiwdtm

A method for finding single-nucleotide polymorphisms with allele frequencies in sequences of deep coverage

Jianmin Wang, Xiaoqiu Huang
2005 BMC Bioinformatics  
Sequence-based methods for finding SNPs with allele frequencies may need to handle thousands of sequences from the same genome location (sequences of deep coverage).  ...  We describe a computational method for finding common SNPs with allele frequencies in single-pass sequences of deep coverage.  ...  Acknowledgements We thank Geo Pertea and John Quackenbush for discussions on assembly of sequences of deep coverage, and Brian Haas for suggestions on and evaluation of GAP22.  ... 
doi:10.1186/1471-2105-6-220 pmid:16146575 pmcid:PMC1239908 fatcat:w4seshahsnedvfhqfvyffpyfky

Anchor points for genome alignment based on Filtered Spaced Word Matches [article]

Chris-Andre Leimeister, Thomas Dencker, Burkhard Morgenstern
2017 arXiv   pre-print
Alignment of large genomic sequences is a fundamental task in computational genome analysis.  ...  Most methods for genomic alignment use high-scoring local alignments as anchor points to reduce the search space of the alignment procedure.  ...  More examples for spaced-words histograms are given in [34] . Our approach to find anchor points for pairwise genomic alignment is as follows.  ... 
arXiv:1703.08792v1 fatcat:dzmqjby2bva2lkuzqfkqilo4ja

GS-Aligner: A Novel Tool for Aligning Genomic Sequences Using Bit-Level Operations

A. C.-C. Shih
2003 Molecular biology and evolution  
It is suitable for aligning fairly divergent sequences such as human and mouse genomic sequences.  ...  GS-Aligner is efficient in terms of both time and space for aligning two very long genomic sequences and for identifying genomic rearrangements such as translocations and inversions.  ...  Acknowledgments We thank Anton Nekrutenko, Haidong Wang, and two reviewers for their valuable suggestions and Wen-Yu Chung for maintenance of the program.  ... 
doi:10.1093/molbev/msg139 pmid:12777500 fatcat:rpiejrkpw5dfvhm3hkjnrrjcca

Comparisons of Long Genomic Sequences [chapter]

Inna Dubchak, Michael Brudno
2005 Chapman & Hall/CRC Computer & Information Science Series  
problems in comparative genomics.  ...  We would like to thank Katya Permiakova for reading an early draft of the chapter and making many useful comments.  ...  The initial approaches for whole genome comparison developed for human and mouse genomes were based either on local alignment [57, 46, 6] , or on a local/global technique, where stretches of one genome  ... 
doi:10.1201/9781420036275.pt4 fatcat:jjjsnbomcbanvh54dxaf2n4qka

Mugsy: fast multiple alignment of closely related whole genomes

Samuel V. Angiuoli, Steven L. Salzberg
2010 Computer applications in the biosciences : CABIOS  
Motivation: The relative ease and low cost of current generation sequencing technologies has led to a dramatic increase in the number of sequenced genomes for species across the tree of life.  ...  Results: We present a new multiple alignment tool for whole genomes named Mugsy.  ...  ACKNOWLEDGEMENTS We thank Herve Tettelin, Jason Stahl, Dave Rasko, Florian Fricke, David Riley and the anonymous reviewers for thoughtful feedback for suggestions.  ... 
doi:10.1093/bioinformatics/btq665 pmid:21148543 pmcid:PMC3031037 fatcat:6776kevbdreabl347q6pmcq7gu
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