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Article ; Online: MyCLADE: a multi-source domain annotation server for sequence functional exploration.

Vicedomini, Riccardo / Blachon, Clémence / Oteri, Francesco / Carbone, Alessandra

2021 Volume 49, Issue W1, Page(s) W452–W458

Abstract: The ever-increasing number of genomic and metagenomic sequences accumulating in our databases requires accurate approaches to explore their content against specific domain targets. MyCLADE is a user-friendly webserver designed for targeted functional ... ...

Abstract	The ever-increasing number of genomic and metagenomic sequences accumulating in our databases requires accurate approaches to explore their content against specific domain targets. MyCLADE is a user-friendly webserver designed for targeted functional profiling of genomic and metagenomic sequences based on a database of a few million probabilistic models of Pfam domains. It uses the MetaCLADE multi-source domain annotation strategy, modelling domains based on multiple probabilistic profiles. MyCLADE takes a list of protein sequences and possibly a target set of domains/clans as input and, for each sequence, it provides a domain architecture built from the targeted domains or from all Pfam domains. It is linked to the Pfam and QuickGO databases in multiple ways for easy retrieval of domain and clan information. E-value, bit-score, domain-dependent probability scores and logos representing the match of the model with the sequence are provided to help the user to assess the quality of each annotation. Availability and implementation: MyCLADE is freely available at http://www.lcqb.upmc.fr/myclade.
MeSH term(s)	Genomics ; Metagenomics ; Molecular Sequence Annotation ; Protein Domains ; Sequence Analysis, Protein/methods ; Software ; Staphylococcus aureus/genetics
Language	English
Publishing date	2021-05-23
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	186809-3
ISSN	1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
ISSN (online)	1362-4962 ; 1362-4954
ISSN	0301-5610 ; 0305-1048
DOI	10.1093/nar/gkab395
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Article ; Online: aKmerBroom: Ancient oral DNA decontamination using Bloom filters on k-mer sets.

Duitama González, Camila / Rangavittal, Samarth / Vicedomini, Riccardo / Chikhi, Rayan / Richard, Hugues

iScience

2023 Volume 26, Issue 11, Page(s) 108057

Abstract: Dental calculus samples are modeled as a mixture of DNA coming from dental plaque and contaminants. Current computational decontamination methods such as Recentrifuge and DeconSeq require either a reference database or sequenced negative controls, and ... ...

Abstract	Dental calculus samples are modeled as a mixture of DNA coming from dental plaque and contaminants. Current computational decontamination methods such as Recentrifuge and DeconSeq require either a reference database or sequenced negative controls, and therefore have limited use cases. We present a reference-free decontamination tool tailored for the removal of contaminant DNA of ancient oral sample called aKmerBroom. Our tool builds a Bloom filter of known ancient and modern oral k-mers, then scans an input set of ancient metagenomic reads using multiple passes to iteratively retain reads likely to be of oral origin. On synthetic data, aKmerBroom achieves over
Language	English
Publishing date	2023-09-29
Publishing country	United States
Document type	Journal Article
ISSN	2589-0042
ISSN (online)	2589-0042
DOI	10.1016/j.isci.2023.108057
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Article ; Online: decOM: similarity-based microbial source tracking of ancient oral samples using k-mer-based methods.

Duitama González, Camila / Vicedomini, Riccardo / Lemane, Téo / Rascovan, Nicolas / Richard, Hugues / Chikhi, Rayan

Microbiome

2023 Volume 11, Issue 1, Page(s) 243

Abstract: Background: The analysis of ancient oral metagenomes from archaeological human and animal samples is largely confounded by contaminant DNA sequences from modern and environmental sources. Existing methods for Microbial Source Tracking (MST) estimate the ...

Abstract	Background: The analysis of ancient oral metagenomes from archaeological human and animal samples is largely confounded by contaminant DNA sequences from modern and environmental sources. Existing methods for Microbial Source Tracking (MST) estimate the proportions of environmental sources, but do not perform well on ancient metagenomes. We developed a novel method called decOM for Microbial Source Tracking and classification of ancient and modern metagenomic samples using k-mer matrices. Results: We analysed a collection of 360 ancient oral, modern oral, sediment/soil and skin metagenomes, using stratified five-fold cross-validation. decOM estimates the contributions of these source environments in ancient oral metagenomic samples with high accuracy, outperforming two state-of-the-art methods for source tracking, FEAST and mSourceTracker. Conclusions: decOM is a high-accuracy microbial source tracking method, suitable for ancient oral metagenomic data sets. The decOM method is generic and could also be adapted for MST of other ancient and modern types of metagenomes. We anticipate that decOM will be a valuable tool for MST of ancient metagenomic studies. Video Abstract.
MeSH term(s)	Animals ; Humans ; Metagenome ; Metagenomics/methods
Language	English
Publishing date	2023-11-06
Publishing country	England
Document type	Video-Audio Media ; Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2697425-3
ISSN	2049-2618 ; 2049-2618
ISSN (online)	2049-2618
ISSN	2049-2618
DOI	10.1186/s40168-023-01670-3
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Article ; Online: Targeted domain assembly for fast functional profiling of metagenomic datasets with S3A.

David, Laurent / Vicedomini, Riccardo / Richard, Hugues / Carbone, Alessandra

Bioinformatics (Oxford, England)

2020 Volume 36, Issue 13, Page(s) 3975–3981

Abstract: Motivation: The understanding of the ever-increasing number of metagenomic sequences accumulating in our databases demands for approaches that rapidly 'explore' the content of multiple and/or large metagenomic datasets with respect to specific domain ... ...

Abstract	Motivation: The understanding of the ever-increasing number of metagenomic sequences accumulating in our databases demands for approaches that rapidly 'explore' the content of multiple and/or large metagenomic datasets with respect to specific domain targets, avoiding full domain annotation and full assembly. Results: S3A is a fast and accurate domain-targeted assembler designed for a rapid functional profiling. It is based on a novel construction and a fast traversal of the Overlap-Layout-Consensus graph, designed to reconstruct coding regions from domain annotated metagenomic sequence reads. S3A relies on high-quality domain annotation to efficiently assemble metagenomic sequences and on the design of a new confidence measure for a fast evaluation of overlapping reads. Its implementation is highly generic and can be applied to any arbitrary type of annotation. On simulated data, S3A achieves a level of accuracy similar to that of classical metagenomics assembly tools while permitting to conduct a faster and sensitive profiling on domains of interest. When studying a few dozens of functional domains-a typical scenario-S3A is up to an order of magnitude faster than general purpose metagenomic assemblers, thus enabling the analysis of a larger number of datasets in the same amount of time. S3A opens new avenues to the fast exploration of the rapidly increasing number of metagenomic datasets displaying an ever-increasing size. Availability and implementation: S3A is available at http://www.lcqb.upmc.fr/S3A_ASSEMBLER/. Supplementary information: Supplementary data are available at Bioinformatics online.
MeSH term(s)	Algorithms ; Metagenome ; Metagenomics ; Sequence Analysis, DNA ; Software
Language	English
Publishing date	2020-04-24
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1422668-6
ISSN	1367-4811 ; 1367-4803
ISSN (online)	1367-4811
ISSN	1367-4803
DOI	10.1093/bioinformatics/btaa272
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Article ; Online: Strainberry: automated strain separation in low-complexity metagenomes using long reads.

Vicedomini, Riccardo / Quince, Christopher / Darling, Aaron E / Chikhi, Rayan

Nature communications

2021 Volume 12, Issue 1, Page(s) 4485

Abstract: High-throughput short-read metagenomics has enabled large-scale species-level analysis and functional characterization of microbial communities. Microbiomes often contain multiple strains of the same species, and different strains have been shown to have ...

Abstract	High-throughput short-read metagenomics has enabled large-scale species-level analysis and functional characterization of microbial communities. Microbiomes often contain multiple strains of the same species, and different strains have been shown to have important differences in their functional roles. Recent advances on long-read based methods enabled accurate assembly of bacterial genomes from complex microbiomes and an as-yet-unrealized opportunity to resolve strains. Here we present Strainberry, a metagenome assembly pipeline that performs strain separation in single-sample low-complexity metagenomes and that relies uniquely on long-read data. We benchmarked Strainberry on mock communities for which it produces strain-resolved assemblies with near-complete reference coverage and 99.9% base accuracy. We also applied Strainberry on real datasets for which it improved assemblies generating 20-118% additional genomic material than conventional metagenome assemblies on individual strain genomes. We show that Strainberry is also able to refine microbial diversity in a complex microbiome, with complete separation of strain genomes. We anticipate this work to be a starting point for further methodological improvements on strain-resolved metagenome assembly in environments of higher complexities.
MeSH term(s)	Bacteria/classification ; Bacteria/genetics ; Computational Biology/methods ; Genome, Bacterial/genetics ; Genomics/methods ; High-Throughput Nucleotide Sequencing ; Metagenome/genetics ; Metagenomics/methods ; Species Specificity
Language	English
Publishing date	2021-07-23
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-021-24515-9
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Article ; Online: A multi-source domain annotation pipeline for quantitative metagenomic and metatranscriptomic functional profiling.

Ugarte, Ari / Vicedomini, Riccardo / Bernardes, Juliana / Carbone, Alessandra

Microbiome

2018 Volume 6, Issue 1, Page(s) 149

Abstract: Background: Biochemical and regulatory pathways have until recently been thought and modelled within one cell type, one organism and one species. This vision is being dramatically changed by the advent of whole microbiome sequencing studies, revealing ... ...

Abstract	Background: Biochemical and regulatory pathways have until recently been thought and modelled within one cell type, one organism and one species. This vision is being dramatically changed by the advent of whole microbiome sequencing studies, revealing the role of symbiotic microbial populations in fundamental biochemical functions. The new landscape we face requires the reconstruction of biochemical and regulatory pathways at the community level in a given environment. In order to understand how environmental factors affect the genetic material and the dynamics of the expression from one environment to another, we want to evaluate the quantity of gene protein sequences or transcripts associated to a given pathway by precisely estimating the abundance of protein domains, their weak presence or absence in environmental samples. Results: MetaCLADE is a novel profile-based domain annotation pipeline based on a multi-source domain annotation strategy. It applies directly to reads and improves identification of the catalog of functions in microbiomes. MetaCLADE is applied to simulated data and to more than ten metagenomic and metatranscriptomic datasets from different environments where it outperforms InterProScan in the number of annotated domains. It is compared to the state-of-the-art non-profile-based and profile-based methods, UProC and HMM-GRASPx, showing complementary predictions to UProC. A combination of MetaCLADE and UProC improves even further the functional annotation of environmental samples. Conclusions: Learning about the functional activity of environmental microbial communities is a crucial step to understand microbial interactions and large-scale environmental impact. MetaCLADE has been explicitly designed for metagenomic and metatranscriptomic data and allows for the discovery of patterns in divergent sequences, thanks to its multi-source strategy. MetaCLADE highly improves current domain annotation methods and reaches a fine degree of accuracy in annotation of very different environments such as soil and marine ecosystems, ancient metagenomes and human tissues.
MeSH term(s)	Algorithms ; Bacteria/classification ; Bacteria/genetics ; Bacteria/isolation & purification ; Bacterial Proteins/chemistry ; Bacterial Proteins/genetics ; Bacterial Proteins/metabolism ; Databases, Genetic ; Environmental Microbiology ; Gastrointestinal Microbiome ; Humans ; Metagenome ; Metagenomics/methods ; Molecular Sequence Annotation/methods ; Protein Domains
Chemical Substances	Bacterial Proteins
Language	English
Publishing date	2018-08-28
Publishing country	England
Document type	Evaluation Studies ; Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2697425-3
ISSN	2049-2618 ; 2049-2618
ISSN (online)	2049-2618
ISSN	2049-2618
DOI	10.1186/s40168-018-0532-2
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Article ; Online: GAM-NGS: genomic assemblies merger for next generation sequencing.

Vicedomini, Riccardo / Vezzi, Francesco / Scalabrin, Simone / Arvestad, Lars / Policriti, Alberto

BMC bioinformatics

2013 Volume 14 Suppl 7, Page(s) S6

Abstract: Background: In recent years more than 20 assemblers have been proposed to tackle the hard task of assembling NGS data. A common heuristic when assembling a genome is to use several assemblers and then select the best assembly according to some criteria. ...

Abstract	Background: In recent years more than 20 assemblers have been proposed to tackle the hard task of assembling NGS data. A common heuristic when assembling a genome is to use several assemblers and then select the best assembly according to some criteria. However, recent results clearly show that some assemblers lead to better statistics than others on specific regions but are outperformed on other regions or on different evaluation measures. To limit these problems we developed GAM-NGS (Genomic Assemblies Merger for Next Generation Sequencing), whose primary goal is to merge two or more assemblies in order to enhance contiguity and correctness of both. GAM-NGS does not rely on global alignment: regions of the two assemblies representing the same genomic locus (called blocks) are identified through reads' alignments and stored in a weighted graph. The merging phase is carried out with the help of this weighted graph that allows an optimal resolution of local problematic regions. Results: GAM-NGS has been tested on six different datasets and compared to other assembly reconciliation tools. The availability of a reference sequence for three of them allowed us to show how GAM-NGS is a tool able to output an improved reliable set of sequences. GAM-NGS is also a very efficient tool able to merge assemblies using substantially less computational resources than comparable tools. In order to achieve such goals, GAM-NGS avoids global alignment between contigs, making its strategy unique among other assembly reconciliation tools. Conclusions: The difficulty to obtain correct and reliable assemblies using a single assembler is forcing the introduction of new algorithms able to enhance de novo assemblies. GAM-NGS is a tool able to merge two or more assemblies in order to improve contiguity and correctness. It can be used on all NGS-based assembly projects and it shows its full potential with multi-library Illumina-based projects. With more than 20 available assemblers it is hard to select the best tool. In this context we propose a tool that improves assemblies (and, as a by-product, perhaps even assemblers) by merging them and selecting the generating that is most likely to be correct.
MeSH term(s)	Algorithms ; Chromosomes/genetics ; Genome, Bacterial ; Genome, Human ; High-Throughput Nucleotide Sequencing ; Humans ; Rhodobacter sphaeroides/genetics ; Sequence Analysis, DNA/methods ; Software ; Staphylococcus aureus/genetics
Language	English
Publishing date	2013-04-22
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2041484-5
ISSN	1471-2105 ; 1471-2105
ISSN (online)	1471-2105
ISSN	1471-2105
DOI	10.1186/1471-2105-14-S7-S6
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Article ; Online: Critical Assessment of Metagenome Interpretation: the second round of challenges.

Meyer, Fernando / Fritz, Adrian / Deng, Zhi-Luo / Koslicki, David / Lesker, Till Robin / Gurevich, Alexey / Robertson, Gary / Alser, Mohammed / Antipov, Dmitry / Beghini, Francesco / Bertrand, Denis / Brito, Jaqueline J / Brown, C Titus / Buchmann, Jan / Buluç, Aydin / Chen, Bo / Chikhi, Rayan / Clausen, Philip T L C / Cristian, Alexandru /

Dabrowski, Piotr Wojciech / Darling, Aaron E / Egan, Rob / Eskin, Eleazar / Georganas, Evangelos / Goltsman, Eugene / Gray, Melissa A / Hansen, Lars Hestbjerg / Hofmeyr, Steven / Huang, Pingqin / Irber, Luiz / Jia, Huijue / Jørgensen, Tue Sparholt / Kieser, Silas D / Klemetsen, Terje / Kola, Axel / Kolmogorov, Mikhail / Korobeynikov, Anton / Kwan, Jason / LaPierre, Nathan / Lemaitre, Claire / Li, Chenhao / Limasset, Antoine / Malcher-Miranda, Fabio / Mangul, Serghei / Marcelino, Vanessa R / Marchet, Camille / Marijon, Pierre / Meleshko, Dmitry / Mende, Daniel R / Milanese, Alessio / Nagarajan, Niranjan / Nissen, Jakob / Nurk, Sergey / Oliker, Leonid / Paoli, Lucas / Peterlongo, Pierre / Piro, Vitor C / Porter, Jacob S / Rasmussen, Simon / Rees, Evan R / Reinert, Knut / Renard, Bernhard / Robertsen, Espen Mikal / Rosen, Gail L / Ruscheweyh, Hans-Joachim / Sarwal, Varuni / Segata, Nicola / Seiler, Enrico / Shi, Lizhen / Sun, Fengzhu / Sunagawa, Shinichi / Sørensen, Søren Johannes / Thomas, Ashleigh / Tong, Chengxuan / Trajkovski, Mirko / Tremblay, Julien / Uritskiy, Gherman / Vicedomini, Riccardo / Wang, Zhengyang / Wang, Ziye / Wang, Zhong / Warren, Andrew / Willassen, Nils Peder / Yelick, Katherine / You, Ronghui / Zeller, Georg / Zhao, Zhengqiao / Zhu, Shanfeng / Zhu, Jie / Garrido-Oter, Ruben / Gastmeier, Petra / Hacquard, Stephane / Häußler, Susanne / Khaledi, Ariane / Maechler, Friederike / Mesny, Fantin / Radutoiu, Simona / Schulze-Lefert, Paul / Smit, Nathiana / Strowig, Till / Bremges, Andreas / Sczyrba, Alexander / McHardy, Alice Carolyn

Nature methods

2022 Volume 19, Issue 4, Page(s) 429–440

Abstract: Evaluating metagenomic software is key for optimizing metagenome interpretation and focus of the Initiative for the Critical Assessment of Metagenome Interpretation (CAMI). The CAMI II challenge engaged the community to assess methods on realistic and ... ...

Abstract	Evaluating metagenomic software is key for optimizing metagenome interpretation and focus of the Initiative for the Critical Assessment of Metagenome Interpretation (CAMI). The CAMI II challenge engaged the community to assess methods on realistic and complex datasets with long- and short-read sequences, created computationally from around 1,700 new and known genomes, as well as 600 new plasmids and viruses. Here we analyze 5,002 results by 76 program versions. Substantial improvements were seen in assembly, some due to long-read data. Related strains still were challenging for assembly and genome recovery through binning, as was assembly quality for the latter. Profilers markedly matured, with taxon profilers and binners excelling at higher bacterial ranks, but underperforming for viruses and Archaea. Clinical pathogen detection results revealed a need to improve reproducibility. Runtime and memory usage analyses identified efficient programs, including top performers with other metrics. The results identify challenges and guide researchers in selecting methods for analyses.
MeSH term(s)	Archaea/genetics ; Metagenome ; Metagenomics/methods ; Reproducibility of Results ; Sequence Analysis, DNA ; Software
Language	English
Publishing date	2022-04-08
Publishing country	United States
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, Non-U.S. Gov't
ZDB-ID	2169522-2
ISSN	1548-7105 ; 1548-7091
ISSN (online)	1548-7105
ISSN	1548-7091
DOI	10.1038/s41592-022-01431-4
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Article ; Online: The Norway spruce genome sequence and conifer genome evolution.

Nystedt, Björn / Street, Nathaniel R / Wetterbom, Anna / Zuccolo, Andrea / Lin, Yao-Cheng / Scofield, Douglas G / Vezzi, Francesco / Delhomme, Nicolas / Giacomello, Stefania / Alexeyenko, Andrey / Vicedomini, Riccardo / Sahlin, Kristoffer / Sherwood, Ellen / Elfstrand, Malin / Gramzow, Lydia / Holmberg, Kristina / Hällman, Jimmie / Keech, Olivier / Klasson, Lisa /

Koriabine, Maxim / Kucukoglu, Melis / Käller, Max / Luthman, Johannes / Lysholm, Fredrik / Niittylä, Totte / Olson, Ake / Rilakovic, Nemanja / Ritland, Carol / Rosselló, Josep A / Sena, Juliana / Svensson, Thomas / Talavera-López, Carlos / Theißen, Günter / Tuominen, Hannele / Vanneste, Kevin / Wu, Zhi-Qiang / Zhang, Bo / Zerbe, Philipp / Arvestad, Lars / Bhalerao, Rishikesh / Bohlmann, Joerg / Bousquet, Jean / Garcia Gil, Rosario / Hvidsten, Torgeir R / de Jong, Pieter / MacKay, John / Morgante, Michele / Ritland, Kermit / Sundberg, Björn / Thompson, Stacey Lee / Van de Peer, Yves / Andersson, Björn / Nilsson, Ove / Ingvarsson, Pär K / Lundeberg, Joakim / Jansson, Stefan

Nature

2013 Volume 497, Issue 7451, Page(s) 579–584

Abstract: Conifers have dominated forests for more than 200 million years and are of huge ecological and economic importance. Here we present the draft assembly of the 20-gigabase genome of Norway spruce (Picea abies), the first available for any gymnosperm. The ... ...

Abstract	Conifers have dominated forests for more than 200 million years and are of huge ecological and economic importance. Here we present the draft assembly of the 20-gigabase genome of Norway spruce (Picea abies), the first available for any gymnosperm. The number of well-supported genes (28,354) is similar to the >100 times smaller genome of Arabidopsis thaliana, and there is no evidence of a recent whole-genome duplication in the gymnosperm lineage. Instead, the large genome size seems to result from the slow and steady accumulation of a diverse set of long-terminal repeat transposable elements, possibly owing to the lack of an efficient elimination mechanism. Comparative sequencing of Pinus sylvestris, Abies sibirica, Juniperus communis, Taxus baccata and Gnetum gnemon reveals that the transposable element diversity is shared among extant conifers. Expression of 24-nucleotide small RNAs, previously implicated in transposable element silencing, is tissue-specific and much lower than in other plants. We further identify numerous long (>10,000 base pairs) introns, gene-like fragments, uncharacterized long non-coding RNAs and short RNAs. This opens up new genomic avenues for conifer forestry and breeding.
MeSH term(s)	Conserved Sequence/genetics ; DNA Transposable Elements/genetics ; Evolution, Molecular ; Gene Silencing ; Genes, Plant/genetics ; Genome, Plant/genetics ; Genomics ; Internet ; Introns/genetics ; Phenotype ; Picea/genetics ; RNA, Untranslated/genetics ; Sequence Analysis, DNA ; Terminal Repeat Sequences/genetics ; Transcription, Genetic/genetics
Chemical Substances	DNA Transposable Elements ; RNA, Untranslated
Language	English
Publishing date	2013-05-22
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	120714-3
ISSN	1476-4687 ; 0028-0836
ISSN (online)	1476-4687
ISSN	0028-0836
DOI	10.1038/nature12211
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Article: Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species.

Bradnam, Keith R / Fass, Joseph N / Alexandrov, Anton / Baranay, Paul / Bechner, Michael / Birol, Inanç / Boisvert, Sébastien / Chapman, Jarrod A / Chapuis, Guillaume / Chikhi, Rayan / Chitsaz, Hamidreza / Chou, Wen-Chi / Corbeil, Jacques / Del Fabbro, Cristian / Docking, T Roderick / Durbin, Richard / Earl, Dent / Emrich, Scott / Fedotov, Pavel /

Fonseca, Nuno A / Ganapathy, Ganeshkumar / Gibbs, Richard A / Gnerre, Sante / Godzaridis, Elénie / Goldstein, Steve / Haimel, Matthias / Hall, Giles / Haussler, David / Hiatt, Joseph B / Ho, Isaac Y / Howard, Jason / Hunt, Martin / Jackman, Shaun D / Jaffe, David B / Jarvis, Erich D / Jiang, Huaiyang / Kazakov, Sergey / Kersey, Paul J / Kitzman, Jacob O / Knight, James R / Koren, Sergey / Lam, Tak-Wah / Lavenier, Dominique / Laviolette, François / Li, Yingrui / Li, Zhenyu / Liu, Binghang / Liu, Yue / Luo, Ruibang / Maccallum, Iain / Macmanes, Matthew D / Maillet, Nicolas / Melnikov, Sergey / Naquin, Delphine / Ning, Zemin / Otto, Thomas D / Paten, Benedict / Paulo, Octávio S / Phillippy, Adam M / Pina-Martins, Francisco / Place, Michael / Przybylski, Dariusz / Qin, Xiang / Qu, Carson / Ribeiro, Filipe J / Richards, Stephen / Rokhsar, Daniel S / Ruby, J Graham / Scalabrin, Simone / Schatz, Michael C / Schwartz, David C / Sergushichev, Alexey / Sharpe, Ted / Shaw, Timothy I / Shendure, Jay / Shi, Yujian / Simpson, Jared T / Song, Henry / Tsarev, Fedor / Vezzi, Francesco / Vicedomini, Riccardo / Vieira, Bruno M / Wang, Jun / Worley, Kim C / Yin, Shuangye / Yiu, Siu-Ming / Yuan, Jianying / Zhang, Guojie / Zhang, Hao / Zhou, Shiguo / Korf, Ian F

GigaScience

2013 Volume 2, Issue 1, Page(s) 10

Abstract: Background: The process of generating raw genome sequence data continues to become cheaper, faster, and more accurate. However, assembly of such data into high-quality, finished genome sequences remains challenging. Many genome assembly tools are ... ...

Abstract	Background: The process of generating raw genome sequence data continues to become cheaper, faster, and more accurate. However, assembly of such data into high-quality, finished genome sequences remains challenging. Many genome assembly tools are available, but they differ greatly in terms of their performance (speed, scalability, hardware requirements, acceptance of newer read technologies) and in their final output (composition of assembled sequence). More importantly, it remains largely unclear how to best assess the quality of assembled genome sequences. The Assemblathon competitions are intended to assess current state-of-the-art methods in genome assembly. Results: In Assemblathon 2, we provided a variety of sequence data to be assembled for three vertebrate species (a bird, a fish, and snake). This resulted in a total of 43 submitted assemblies from 21 participating teams. We evaluated these assemblies using a combination of optical map data, Fosmid sequences, and several statistical methods. From over 100 different metrics, we chose ten key measures by which to assess the overall quality of the assemblies. Conclusions: Many current genome assemblers produced useful assemblies, containing a significant representation of their genes and overall genome structure. However, the high degree of variability between the entries suggests that there is still much room for improvement in the field of genome assembly and that approaches which work well in assembling the genome of one species may not necessarily work well for another.
Language	English
Publishing date	2013-07-22
Publishing country	United States
Document type	Journal Article
ZDB-ID	2708999-X
ISSN	2047-217X
ISSN	2047-217X
DOI	10.1186/2047-217X-2-10
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