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InterProScan 5: genome-scale protein function classification

P. Jones, D. Binns, H.-Y. Chang, M. Fraser, W. Li, C. McAnulla, H. McWilliam, J. Maslen, A. Mitchell, G. Nuka, S. Pesseat, A. F. Quinn (+5 others)
2014 Bioinformatics  
Here, we describe a new Java-based architecture for the widely used protein function prediction software package InterProScan.  ...  Motivation: Robust large-scale sequence analysis is a major challenge in modern genomic science, where biologists are frequently trying to characterize many millions of sequences.  ...  New to InterProScan 5 is the ability to function on a massive scale, to allow the analysis and persistence of match data for millions of sequences under the control of a single 'Master' process with a  ... 
doi:10.1093/bioinformatics/btu031 pmid:24451626 pmcid:PMC3998142 fatcat:kfovtogftvhpbhuwmulywlixha

IPRStats: visualization of the functional potential of an InterProScan run

Ryan J Kelly, David E Vincent, Iddo Friedberg
2010 BMC Bioinformatics  
InterPro is a collection of protein signatures for the classification and automated annotation of proteins.  ...  However, when performing whole-genome or metagenome analysis, there is a need for a fast statistical visualization of the results to have good initial grasp on the functional potential of the sequences  ...  For those reasons, Interproscan [5] is a popular function annotation program.  ... 
doi:10.1186/1471-2105-11-s12-s13 pmid:21210980 pmcid:PMC3040527 fatcat:uhj3l6mw6nesvecjpnhcrryxum

Development of Information Biology (III)

Yoshio Tateno
2013 Interdisciplinary Bio Central  
The second case shows how to elucidate the function of an unknown DNA sequence or ORF in prokaryotes by a large -scale computer homology search and analyses.  ...  The outcome has revealed that the cause of human cancer is located in the genome in a dormant condition.  ...  The classification took a very long CPU time even by using a large-scale computer.  ... 
doi:10.4051/ibc.2013.5.2.0005 fatcat:f6gg4xkc6famzh77ch47dfmtl4

A biophysical approach to large-scale protein-DNA binding data [chapter]

T. Manke, H. Roider, M. Vingron
2008 Modern Genome Annotation  
annotation 155 5.3.1 InterProScan 155 5.3.2 Interpreting InterProScan results 156 5.3.3 Large-scale automatic annotation 159 6 From genes and proteins to genomes and proteomes 160 7 Summary 161  ...  protein signature databases 154 5.1.5 ProDom sequence clustering method 154 5.2 InterPro -integration of protein signature databases 154 5.3 Using InterProScan for sequence classification and functional  ... 
doi:10.1007/978-3-211-75123-7_5 fatcat:z6aywufyprdmpgs5d2xf6dmtx4

From gene expression profiling to gene regulation [chapter]

R. Coulson, T. Manke, K. Palin, H. Roider, O. Sand, J. van Helden, E. Ukkonen, M. Vingron, A. Brazma
2008 Modern Genome Annotation  
annotation 155 5.3.1 InterProScan 155 5.3.2 Interpreting InterProScan results 156 5.3.3 Large-scale automatic annotation 159 6 From genes and proteins to genomes and proteomes 160 7 Summary 161  ...  protein signature databases 154 5.1.5 ProDom sequence clustering method 154 5.2 InterPro -integration of protein signature databases 154 5.3 Using InterProScan for sequence classification and functional  ... 
doi:10.1007/978-3-211-75123-7_6 fatcat:qggfloahxzemrp34hqdo6s3uaa

PlantTFcat: an online plant transcription factor and transcriptional regulator categorization and analysis tool

Xinbin Dai, Senjuti Sinharoy, Michael Udvardi, Patrick Zhao
2013 BMC Bioinformatics  
systematically analyzing InterProScan domain patterns in protein sequences.  ...  Results: Here, we present PlantTFcat, a high-performance web-based analysis tool that is designed to identify and categorize plant TF/TR/CR genes from genome-scale protein and nucleic acid sequences by  ...  To provide high-throughput genome-scale analysis capability, we customized InterProScan to include only relevant domain information.  ... 
doi:10.1186/1471-2105-14-321 pmid:24219505 pmcid:PMC4225725 fatcat:uw4xjfxfqrfnpdd6juil5tzclm

MicrobeAnnotator: a user-friendly, comprehensive functional annotation pipeline for microbial genomes

Carlos A. Ruiz-Perez, Roth E. Conrad, Konstantinos T. Konstantinidis
2021 BMC Bioinformatics  
Results Here, we introduce MicrobeAnnotator, a fully automated, easy-to-use pipeline for the comprehensive functional annotation of microbial genomes that combines results from several reference protein  ...  Accordingly, fast and comprehensive functional gene annotation pipelines are needed to analyze and compare these genomes.  ...  Acknowledgements The authors thank Luis Miguel Rodriguez for their comments and suggestions on functionality and documentation of MicrobeAnnotator.  ... 
doi:10.1186/s12859-020-03940-5 pmid:33407081 fatcat:vbqo3dwn2fenzceptgt4f4uggq

SECOM: A Novel Hash Seed and Community Detection Based-Approach for Genome-Scale Protein Domain Identification

Ming Fan, Ka-Chun Wong, Taewoo Ryu, Timothy Ravasi, Xin Gao, Annalisa Pastore
2012 PLoS ONE  
The functional annotation and evolutionary history of proteins are usually inferred from domains predicted from the genome sequences.  ...  Instead of conducting all-against-all sequence alignment, SECOM first indexes all the proteins in the genome by using a hash seed function.  ...  Here, we propose SECOM, a powerful, novel tool that automatically identifies protein domains at a genome-wide scale.  ... 
doi:10.1371/journal.pone.0039475 pmid:22761802 pmcid:PMC3386278 fatcat:6szpfrjlijdz5eh4ltx7y2hh4e

LegumeIP: an integrative database for comparative genomics and transcriptomics of model legumes

J. Li, X. Dai, T. Liu, P. X. Zhao
2011 Nucleic Acids Research  
based on UniProt, InterProScan, Gene Ontology and the Kyoto Encyclopedia of Genes and Genomes databases.  ...  We present LegumeIP (http://plantgrn.noble.org/ LegumeIP/), an integrative database for comparative genomics and transcriptomics of model legumes, for studying gene function and genome evolution in legumes  ...  To better study gene function and genome evolution, two groups of putative gene families were constructed in the five species based on protein-coding sequence similarity.  ... 
doi:10.1093/nar/gkr939 pmid:22110036 pmcid:PMC3245131 fatcat:v4qytxzf3rexlf2djcjhraprbe

The Porcelain Crab Transcriptome and PCAD, the Porcelain Crab Microarray and Sequence Database

Abderrahmane Tagmount, Mei Wang, Erika Lindquist, Yoshihiro Tanaka, Kristen S. Teranishi, Shinichi Sunagawa, Mike Wong, Jonathon H. Stillman, Samir K. Brahmachari
2010 PLoS ONE  
With the emergence of a completed genome sequence of the freshwater crustacean Daphnia pulex, construction of genomic-scale sequence databases for additional crustacean sequences are important for comparative  ...  genomics and annotation.  ...  some of the InterProScan homology results allow protein classification when BLAST does not.  ... 
doi:10.1371/journal.pone.0009327 pmid:20174471 pmcid:PMC2824831 fatcat:tg4zdfybr5a4ro4bdd6jxf45ua

Workflows for Rapid Functional Annotation of Diverse Arthropod Genomes

Surya Saha, Amanda M. Cooksey, Anna K. Childers, Monica F. Poelchau, Fiona M. McCarthy
2021 Insects  
Genome-scale functional annotation is required for functional modeling (enrichment, networks, etc.).  ...  We present an open-source, open access, and containerized pipeline for genome-scale functional annotation of insect proteomes and apply it to various arthropod species.  ...  . 5 GOanna and InterProScan results for arthropod genomes selected for this study.  ... 
doi:10.3390/insects12080748 fatcat:2metyqt7mrbrloyllelr3swtle

The Repertoires of Ubiquitinating and Deubiquitinating Enzymes in Eukaryotic Genomes

Andrew Paul Hutchins, Shaq Liu, Diego Diez, Diego Miranda-Saavedra
2013 Molecular biology and evolution  
Reversible protein ubiquitination regulates virtually all known cellular activities.  ...  Our method relies on a collection of profile hidden Markov models, and we demonstrate its superior performance (coverage and classification accuracy >99%) by identifying approximately 25% and approximately  ...  OrthoMCL is a sensitive genome-scale algorithm for grouping orthologous protein sequences, with release 5 featuring approximately 1.4 million sequences from 150 genomes (including 57 unikonts, 13 excavates  ... 
doi:10.1093/molbev/mst022 pmid:23393154 pmcid:PMC3670738 fatcat:oowgk7m2cfbqtno3m35uqwyxmy

CyanoBase: the cyanobacteria genome database update 2010

Mitsuteru Nakao, Shinobu Okamoto, Mitsuyo Kohara, Tsunakazu Fujishiro, Takatomo Fujisawa, Shusei Sato, Satoshi Tabata, Takakazu Kaneko, Yasukazu Nakamura
2009 Nucleic Acids Research  
CyanoBase (http://genome.kazusa.or.jp/cyanobase) is the genome database for cyanobacteria, which are model organisms for photosynthesis.  ...  The database houses cyanobacteria species information, complete genome sequences, genomescale experiment data, gene information, gene annotations and mutant information.  ...  In addition, various genome scale experimental datasets have been produced, including gene expression profiles and protein-protein interaction data.  ... 
doi:10.1093/nar/gkp915 pmid:19880388 pmcid:PMC2808859 fatcat:6j2y4xhhdvhm7e547vioiobdr4

RGAugury: a pipeline for genome-wide prediction of resistance gene analogs (RGAs) in plants

Pingchuan Li, Xiande Quan, Gaofeng Jia, Jin Xiao, Sylvie Cloutier, Frank M. You
2016 BMC Genomics  
A user-friendly and efficient pipeline is needed for large-scale genome-wide RGA predictions of the growing number of sequenced plant genomes.  ...  Conclusions: RGAugury is an efficiently integrative bioinformatics tool for large scale genome-wide identification of RGAs. It is freely available at Bitbucket: https://bitbucket.org/yaanlpc/rgaugury.  ...  Panther is a large protein database for comprehensive protein evolutionary and functional classification that contains more than 12,000 protein families from 104 sequenced genomes [45] .  ... 
doi:10.1186/s12864-016-3197-x pmid:27806688 pmcid:PMC5093994 fatcat:2hwgoorznfbthl5tor7sgbsqui

Comparative genome analysis and genome evolution of members of the magnaporthaceae family of fungi

Laura H. Okagaki, Joshua K. Sailsbery, Alexander W. Eyre, Ralph A. Dean
2016 BMC Genomics  
Results: A genome-scale comparative study was conducted across 74 fungal genomes to identify clusters of orthologous genes unique to the three Magnaporthaceae species as well as species specific genes.  ...  No correlations between diversifying or purifying selection and distance to repetitive elements or an increased rate of evolution in secreted and small secreted proteins were observed.  ...  LHO was supported by the Tri-institutional Molecular Mycology and Pathogenesis training grant (NIH 5 T32-AI052080-09  ... 
doi:10.1186/s12864-016-2491-y pmid:26911875 pmcid:PMC4766678 fatcat:wnn76vokpbfr3jwffplp4gvprq
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