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A Comprehensive Approach to Clustering of Expressed Human Gene Sequence: The Sequence Tag Alignment and Consensus Knowledge Base

R. T. Miller
1999 Genome Research  
ACKNOWLEDGMENTS We gratefully acknowledge the support of Silicon Graphics Corporation for its generous donation of time on the CRAY-SGI farm.  ...  The magnitude of the whole-body index necessitates the use of high-performance parallel architecture to complete the clustering phase.  ...  We have performed an independent assessment to determine the fidelity of STACK expression clusters.  ... 
doi:10.1101/gr.9.11.1143 pmid:10568754 pmcid:PMC310831 fatcat:2dnct5aoqfdwfhsqdwjiqfvlta

A Computer-Based Method of Selecting Clones for a Full-Length cDNA Project: Simultaneous Collection of Negligibly Redundant and Variant cDNAs

N. Osato
2002 Genome Research  
The full-length sequences of the clones selected by grouping are determined preferentially, and then the sequences selected by clustering are determined.  ...  Therefore, our method is useful for the selection of appropriate representative clones for full-length sequencing, thereby greatly reducing the cost, labor, and time necessary for this process. 4 Corresponding  ...  This study was supported by a research grant for the RIKEN Genome Exploration Research Project from the Ministry of Education, Culture, Sports, Science, and Technology of the Japanese Government to Y.H  ... 
doi:10.1101/gr.75202. fatcat:swy5gts6s5eergbmqhsfk25fgm

A Computer-Based Method of Selecting Clones for a Full-Length cDNA Project: Simultaneous Collection of Negligibly Redundant and Variant cDNAs

N. Osato, M. Itoh, H. Konno, S. Kondo, K. Shibata, P. Carninci, T. Shiraki, A. Shinagawa, T. Arakawa, S. Kikuchi, K. Sato, J. Kawai (+1 others)
2002 Genome Research  
The full-length sequences of the clones selected by grouping are determined preferentially, and then the sequences selected by clustering are determined.  ...  Therefore, our method is useful for the selection of appropriate representative clones for full-length sequencing, thereby greatly reducing the cost, labor, and time necessary for this process. 4 Corresponding  ...  This study was supported by a research grant for the RIKEN Genome Exploration Research Project from the Ministry of Education, Culture, Sports, Science, and Technology of the Japanese Government to Y.H  ... 
doi:10.1101/gr.75202 pmid:12097351 pmcid:PMC186622 fatcat:ipvbabuubvbcriselbipij4boa

A Hybrid Distance Measure for Clustering Expressed Sequence Tags Originating from the Same Gene Family

Keng-Hoong Ng, Chin-Kuan Ho, Somnuk Phon-Amnuaisuk, Zhanjiang Liu
2012 PLoS ONE  
Clustering is a key step in the processing of Expressed Sequence Tags (ESTs). The primary goal of clustering is to put ESTs from the same transcript of a single gene into a unique cluster.  ...  The clustering results provide support for the effectiveness of the proposed hybrid distance measure in solving the clustering problem for ESTs that originate from the same gene family.  ...  Cluster Validity Index In order to evaluate the performance of our proposed distance measure, the validity of the clustering results obtained from the experiments are assessed.  ... 
doi:10.1371/journal.pone.0047216 pmid:23071763 pmcid:PMC3469558 fatcat:hdqebhuxfbbtbcbwprodcnd2lm

EasyCluster: a fast and efficient gene-oriented clustering tool for large-scale transcriptome data

Ernesto Picardi, Flavio Mignone, Graziano Pesole
2009 BMC Bioinformatics  
EasyCluster has also been used to provide a first compilation of gene-oriented clusters in the Ricinus communis oilseed plant for which no Unigene clusters are yet available, as well as an evaluation of  ...  Methods: EasyCluster uses the well-known GMAP program in order to perform a very quick EST-togenome mapping in addition to the detection of reliable splice sites.  ...  We kindly thank Easy Data http://www.genomesdata.com for support and advice in the management of sequence data.  ... 
doi:10.1186/1471-2105-10-s6-s10 pmid:19534735 pmcid:PMC2697633 fatcat:v32ijwqk4fewnk3mcjgp5hzddy

Sampling the Arabidopsis Transcriptome with Massively Parallel Pyrosequencing

A. P.M. Weber, K. L. Weber, K. Carr, C. Wilkerson, J. B. Ohlrogge
2007 Plant Physiology  
Performing a second sequencing run only increased the number of genes identified by 10%, but increased the overall sequence coverage by 50%. (2) Mapping of the ESTs to their predicted full-length transcripts  ...  Although extensively used already for sequencing of genomes, relatively few applications of massively parallel pyrosequencing to transcriptome analysis have been reported.  ...  ACKNOWLEDGMENTS We thank Shari Tjugum-Holland and Jeff Landgraff of the Michigan State University Research Technology Support Facility for assistance with RNA and DNA analysis and DNA sequencing.  ... 
doi:10.1104/pp.107.096677 pmid:17351049 pmcid:PMC1913805 fatcat:4z23p5mz3bgexmfufvkv6igpba

Efficient clustering of large EST data sets on parallel computers

A. Kalyanaraman
2003 Nucleic Acids Research  
To enable fast clustering of large-scale EST data, we developed PaCE (for Parallel Clustering of ESTs), a software program for EST clustering on parallel computers.  ...  the computational work without sacri®cing the quality of clustering, and (iii) use of parallel processing to reduce run-time and facilitate clustering of larger data sets.  ...  Our sincere thanks to Qunfeng Dong for developing the web interface to illustrate our plant EST clustering results at the PlantGDB website.  ... 
doi:10.1093/nar/gkg379 pmid:12771222 pmcid:PMC156714 fatcat:klms2artobbn3n45dfjfb7jwri

Alignment-free sequence comparison: benefits, applications, and tools

Andrzej Zielezinski, Susana Vinga, Jonas Almeida, Wojciech M. Karlowski
2017 Genome Biology  
The strength of these methods makes them particularly useful for next-generation sequencing data processing and analysis.  ...  of recombined sequences.  ...  The performance of each method was assessed using AUC statistics (area under the receiver operating curve; for details about methods see Additional file 3: Supplementary methods).  ... 
doi:10.1186/s13059-017-1319-7 pmid:28974235 pmcid:PMC5627421 fatcat:5s7yd22l7bbmpljqc7fj4cbifm

Generation of a human gene index and its application to disease candidacy Generation of a human gene index and its application to disease candidacy

Alan Christoffels, Alan Christoffels
2001 unpublished
With easy access to technology to generate expressed sequence tags (ESTs), several groups iv The accuracy of the whole-body index was assessed using the genomic sequence for the annotated 599 chromosome  ...  A total of 63.3% of the chromosome 22 genes had significant identity to whole-body index sequences.  ...  The development of a high performance shared memory parallel (SMP) model for D2_CLUSTER required: hardware configuration tuning The high performance NCSA Origin2000 machines are modified weekly with  ... 
fatcat:mtbpwuqacnav3ep7v4ho2zwmoy

High Performance Computing and Algorithm Development: Application of Dataset Development to Algorithm Parameterization

Mario Ricardo, Jonas, Mario Jonas
2006 unpublished
Phrap, the looser clustering algorithms implemented in d2_cluster and the novel tool WCD, produce results which capture the alternatively expressed sequence information.  ...  Availability of dataset: www.sanbi.ac.za/~mario/dataset.tgz iii Declaration: I declare that "High Performance Computing and Algorithm Development: Application of Dataset Development to Algorithm Parameterization  ...  The high contig-to-singlet ratio for phrap, and cluster-to-singleton ratio for d2_cluster and WCD are mostly due to the lower number of singlets/ singletons.  ... 
fatcat:uygkh6sifffzxdgzvuo2l32uwi

Identification of tissue-specific, abiotic stress-responsive gene expression patterns in wine grape (Vitis vinifera L.) based on curation and mining of large-scale EST data sets

Richard L Tillett, Ali Ergül, Rebecca L Albion, Karen A Schlauch, Grant R Cramer, John C Cushman
2011 BMC Plant Biology  
Curation to correct annotation errors, clustering and assembly of the berry and leaf ESTs with currently available V. vinifera full-length transcripts and ESTs yielded a total of 13,278 unique sequences  ...  Although roots serve as the first site of perception and/or injury for many types of abiotic stress, EST sequencing in root tissues of wine grape exposed to abiotic stresses has been extremely limited  ...  Carver Biotechnology Center at the University of Illinois at Urbana-Champaign and Agencourt Biosciences, Inc. for providing cDNA library construction and high-throughput EST sequencing services.  ... 
doi:10.1186/1471-2229-11-86 pmid:21592389 pmcid:PMC3224124 fatcat:4kugvrovizc7fp7z6xzcm5uf5y

Bioinformatics analyses for the genomic investigation of plants of agronomic importance

Nunzio D'Agostino
2008
During a critical period of my life, she forgot, neither for a moment, my feelings or my character.  ...  ACKNOWLEDGEMENTS Also to my parents, who are still waiting for me to quit 'fooling around with computers' and despite that they urge me in any way.  ...  Clustering and Assembling The sequences were clustered by the PaCE (Parallel Clustering of ESTs) program (Kalyanaraman et al., 2003) which builds a distributed representation of the generalized suffix  ... 
doi:10.6092/unina/fedoa/1695 fatcat:vcux57vx2nggxfesnddlj67qby

Bioinformatic analysis of transcriptome data: application to helminth parasites

Ranjeeta Menon
2022
With only a few nematode genomes completely sequenced, analysis is carried out with transcriptomic data, which requires a number of computational methods for their pre-processing, clustering, assembly  ...  , from the discovery of novel genes for parasite control with minimum host side effects.  ...  ACKNOWLEDGEMENTS We are grateful to Macquarie University for the award of postgraduate research scholarships.  ... 
doi:10.25949/19438937 fatcat:kqbdkdfs5bbevk6qfxzg4z5gbi

Regulation of seed development in Leguminosae: investigating the role of SNF1-related protein kinase [article]

Ruslana Radchuk, Universitäts- Und Landesbibliothek Sachsen-Anhalt, Martin-Luther Universität
2018
For this approach radioactive labeled cDNA probes were prepared from RNA isolated from embryo of developing seeds of WT (11-21 DAP) and transgenic plant (13-19 DAP), which correspond to the transition  ...  To dissect the SnRK1-antisense phenotype at the molecular level, a search for genes with differential expression patterns in transgenic plant vs WT seeds has been performed using cDNA macroarray analysis  ...  I would like to thank all the co-workers of the Institute, especially from the "Gene Expression" and "Bioinformatics" groups for the scientifically stimulation environment that has promoted this work.  ... 
doi:10.25673/3677 fatcat:6svj2pemxvdzpip47i23ukociu