Filters








1,633 Hits in 5.3 sec

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  
SHRiMP is freely available at http://compbio.cs.toronto.edu/shrimp. Citation: Rumble SM, Lacroute P, Dalca AV, Fiume M, Sidow A, et al. (2009) SHRiMP: Accurate Mapping of Short Color-space Reads.  ...  In this paper we present SHRiMP -the SHort Read Mapping Package: a set of algorithms and methods to map short reads to a genome, even in the presence of a large amount of polymorphism.  ...  Color-space mapping accuracy of SHRiMP. dynamic programming matrix using diagonals.  ... 
doi:10.1371/journal.pcbi.1000386 pmid:19461883 pmcid:PMC2678294 fatcat:xi2byt525vdxbbyr7dwk3phrpu

Pink shrimp as an indicator for restoration of everglades ecosystems

Joan A. Browder, Michael B. Robblee
2009 Ecological Indicators  
Acknowledgments The development and publication of this manuscript was supported by the Task Force Office of the Executive Director (Greg May & Rock Salt), the USGS South Florida Office (Ronnie Best),  ...  We wish to thank the Army Corps of Engineers, Jacksonville for supporting FIAN under Work Orders 19 (USGS and 3 (NOAA).  ...  space.  ... 
doi:10.1016/j.ecolind.2008.10.007 fatcat:dav2oyj4nfgzzdxefacziykutq

Research frontiers in penaeid shrimp reproduction: Future trends to improve commercial production

Jorge Alfaro-Montoya, André Braga, Rodolfo Umaña-Castro
2019 Aquaculture  
This review identified ten reproduction-related research subjects that can improve the shrimp industry based on basic scientific knowledge and four levels of application: eyestalk ablation alternatives  ...  A B S T R A C T Shrimp farming worldwide is based on a similar technological package, characterized by three phases: Controlled Reproduction, Larvae Culture, and Grow-out Culture.  ...  N/A: not available. 1 Whole genome shotgun sequencing by Illumina HiSeq platform. 2 Sanger dideoxy and/or Illumina sequencing. 3 DNA sequencing Illumina HiSeq platform or 454 pyrosequencing. 4 Short Read  ... 
doi:10.1016/j.aquaculture.2018.12.068 fatcat:zpvhuqm2frfbjigpa6hp63kiw4

A unique way of sound production in the snapping shrimp (Alpheus heterochaelis)

Barbara Schmitz, Michel Versluis, Anna von der Heydt, Detlef Lohse
2000 Journal of the Acoustical Society of America  
Both programs were used to produce maps indicating sound levels as color contours which simplified presentation of these data to the client.  ...  Formally, dimension of phase space is a doubled dimension of coordinate space.  ...  One may also judge that the scaling of physical dimension is inappropriate if the mapping function of the physical space to the perceptual space appears to be critically nonlinear.  ... 
doi:10.1121/1.4743419 fatcat:g5t436uevvdzfdqfenskbzrgla

Enterococcus faecium are associated with the modification of gut microbiota and shrimp post-larvae survival

Shicong Du, Wei Chen, Zhiyuan Yao, Xiaolin Huang, Chen Chen, Haipeng Guo, Demin Zhang
2021 Animal Microbiome  
Both Tre and SH showed a low and uneven community species and shorted phylogenetic distance.  ...  In this study, eighteen tanks with eight hundred of shrimp post-larvae individuals each were randomly grouped into three groups, one is shrimps administered with E. faecium as probiotic (Tre) and others  ...  Acknowledgements The authors would like to thank the entire research group in Zhang lab of the Ningbo University.  ... 
doi:10.1186/s42523-021-00152-x pmid:34952650 pmcid:PMC8710032 fatcat:szwqkgjl2neo5le4p36mq6n3zy

Sensitive and fast mapping of di-base encoded reads

F. Hormozdiari, F. Hach, S. C. Sahinalp, E. E. Eichler, C. Alkan
2011 Bioinformatics  
Results: We present drFAST, a read mapper designed for di-base encoded 'color-space' sequences generated with the AB SOLiD platform. drFAST is specially designed for better delineation of structural variants  ...  , including segmental duplications, and is able to return all possible map locations and underlying sequence variation of short reads within a user-specified distance threshold.  ...  Health Research grants (to S.C.S. in parts); US National Institutes of Health (grants HG004120 and HG005209 to E.E.E.).  ... 
doi:10.1093/bioinformatics/btr647 pmcid:PMC3276229 fatcat:rhah2ss57nbnlnahei4vubil5y

Sensitive and fast mapping of di-base encoded reads

F. Hormozdiari, F. Hach, S. C. Sahinalp, E. E. Eichler, C. Alkan
2011 Bioinformatics  
Results: We present drFAST, a read mapper designed for di-base encoded 'color-space' sequences generated with the AB SOLiD platform. drFAST is specially designed for better delineation of structural variants  ...  , including segmental duplications, and is able to return all possible map locations and underlying sequence variation of short reads within a user-specified distance threshold.  ...  Health Research grants (to S.C.S. in parts); US National Institutes of Health (grants HG004120 and HG005209 to E.E.E.).  ... 
doi:10.1093/bioinformatics/btr303 pmid:21586516 pmcid:PMC3129524 fatcat:3pl3auezdbcg7hl7q6rlizptoe

VARiD: A variation detection framework for color-space and letter-space platforms

A. V. Dalca, S. M. Rumble, S. Levy, M. Brudno
2010 Bioinformatics  
Results: We present VARiD-a probabilistic method for variation detection from both letter-and color-space reads simultaneously.  ...  Our analysis shows that VARiD performs better than the AB SOLiD toolset at detecting variants from color-space data alone, and improves the calls dramatically when letter-and color-space reads are combined  ...  Conflict of Interest: none declared.  ... 
doi:10.1093/bioinformatics/btq184 pmid:20529926 pmcid:PMC2881369 fatcat:qnejbeht3rhyzh2ivyewzoftau

BALOs Improved Gut Microbiota Health in Postlarval Shrimp (Litopenaeus vannamei) After Being Subjected to Salinity Reduction Treatment

Qingqing Cao, Farhana Najnine, Hongcao Han, Bing Wu, Junpeng Cai
2020 Frontiers in Microbiology  
In this study, we applied a euryhaline strain of BALOs, BDN-1F2 (BD), and Bacillus subtilis (SD) to the rearing of second-generation shrimp PL after salinity reduction treatment so as to determine if they  ...  White shrimp, Litopenaeus vannamei, is a widely farmed species. In China, shrimp postlarvae (PL) are frequently subjected to salinity reduction treatment to meet end growers' needs.  ...  Different colors represent the extent of strength/richness of a function with a darker red color representing stronger strength (higher richness) and darker blue representing lower richness.  ... 
doi:10.3389/fmicb.2020.01296 pmid:32714290 pmcid:PMC7344170 fatcat:jidaqhdvhfcgzkuo5zmtpxrbl4

Challenges in exome analysis by LifeScope and its alternative computational pipelines

Erinija Pranckevičiene, Tautvydas Rančelis, Aidas Pranculis, Vaidutis Kučinskas
2015 BMC Research Notes  
Our investigated tools comprised proprietary LifeScope's pipeline in combination with open source color-space competent mapping programs and a variant caller.  ...  We observed less than 50 % concordance of variant lists produced by approaches based on different mapping algorithms.  ...  The color-space competent alignment tools often utilized in practice are Blat-like Fast Accurate Search Tool (BFAST), Bowtie, Short Read Mapping Package (SHRiMP) and Mapping and Assembly with Qualities  ... 
doi:10.1186/s13104-015-1385-4 pmid:26346699 pmcid:PMC4562342 fatcat:hk7rbms6mve43emyf3ms3jlkem

Efficient mapping of Applied Biosystems SOLiD sequence data to a reference genome for functional genomic applications

Brian D. Ondov, Anjana Varadarajan, Karla D. Passalacqua, Nicholas H. Bergman
2008 Computer applications in the biosciences : CABIOS  
Here, we report the development of SOCS (short oligonucleotide color space), a program designed for efficient and flexible mapping of Applied Biosystems SOLiD sequence data onto a reference genome.  ...  SOCS performs its mapping within the context of 'color space', and it maximizes usable data by allowing a user-specified number of mismatches.  ...  Conflict of Interest: none declared.  ... 
doi:10.1093/bioinformatics/btn512 pmid:18842598 pmcid:PMC2639273 fatcat:5d46ygbowvafhlaxdcrxw73y7y

BFAST: An Alignment Tool for Large Scale Genome Resequencing

Nils Homer, Barry Merriman, Stanley F. Nelson, Chad Creighton
2009 PLoS ONE  
The new generation of massively parallel DNA sequencers, combined with the challenge of whole human genome resequencing, result in the need for rapid and accurate alignment of billions of short DNA sequence  ...  Speed is obviously of great importance, but equally important is maintaining alignment accuracy of short reads, in the 25-100 base range, in the presence of errors and true biological variation.  ...  We also thank members of the Nelson Lab: Zugen Chen, Hane Lee, Bret Harry, Jordan Mendler, Brian O'Connor and Michael J. Clark for input and computational infrastructure support.  ... 
doi:10.1371/journal.pone.0007767 pmid:19907642 pmcid:PMC2770639 fatcat:4oqad3kplfdstd4ujftpc7gvpq

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.  ...  27 SHRiMP http://compbio.cs.toronto.edu/ shrimp/ Yes Yes Hash the reads SAM output format; supports both letter space and color space reads; allows paired-end reads alignment, parallel computation  ... 
doi:10.1038/jhg.2011.62 pmid:21677664 fatcat:7v3jia5x4rgvrmfzjm5dgncdsy

Designing Efficient Spaced Seeds for SOLiD Read Mapping

Laurent Noé, Marta Gîrdea, Gregory Kucherov
2010 Advances in Bioinformatics  
solution to mapping SOLiD color-space reads to a reference genome.  ...  The solution relies on an advanced method of seed design that uses a faithful probabilistic model of read matches and, on the other hand, a novel seeding principle especially adapted to read mapping.  ...  reads that They used as a testset in their study.  ... 
doi:10.1155/2010/708501 pmid:20936175 pmcid:PMC2945724 fatcat:nahdomgtm5bfpf3pk2mrmifh2i

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

Z. Zhang, H. Lin, B. Ma
2010 Nucleic Acids Research  
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  ...  The software handles both single-end and paired-end reads, and can output both the unique mapping result or the top N mapping results for each read.  ...  Conflict of interest statement. None declared.  ... 
doi:10.1093/nar/gkq538 pmid:20530531 pmcid:PMC2896157 fatcat:qhdobau5unhxhb3hgnzpbsn7ke
« Previous Showing results 1 — 15 out of 1,633 results