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EST2uni: an open, parallel tool for automated EST analysis and database creation, with a data mining web interface and microarray expression data integration

Javier Forment, Francisco Gilabert, Antonio Robles, Vicente Conejero, Fernando Nuez, Jose M Blanca
2008 BMC Bioinformatics  
Results: We have created EST2uni, an integrated, highly-configurable EST analysis pipeline and data mining software package that automates the pre-processing, clustering, annotation, database creation,  ...  Conclusion: The software package presented here provides an efficient and complete bioinformatics tool for the management of EST collections which is very easy to adapt to the local needs of different  ...  Joaquin Dopazo and the Spanish National Institute of Bioinformatics [40], a platform of Genoma España, for providing help to integrate the Babelomics and GEPAS tools in EST2uni.  ... 
doi:10.1186/1471-2105-9-5 pmid:18179701 pmcid:PMC2258287 fatcat:p5smmlediffnnos27ray3u6pli

ESTpass: a web-based server for processing and annotating expressed sequence tag (EST) sequences

B. Lee, T. Hong, S. J. Byun, T. Woo, Y. J. Choi
2007 Nucleic Acids Research  
We present a web-based server, called ESTpass, for processing and annotating sequence data from expressed sequence tag (EST) projects.  ...  ESTpass accepts a FASTA-formatted EST file and its quality file as inputs, and it then executes a back-end EST analysis pipeline consisting of three consecutive steps.  ...  We would like to acknowledge all the members of ESTAP and other EST pipeline teams for making their tools and resources freely available. We thank Maryana Bhak for editing the manuscript.  ... 
doi:10.1093/nar/gkm369 pmid:17526512 pmcid:PMC1933161 fatcat:hkjuk2j6hnf6npeldfz3mvesoy

EST-PAC a web package for EST annotation and protein sequence prediction

Yvan Strahm, David Powell, Christophe Lefèvre
2006 Source Code for Biology and Medicine  
The system allows users to customize annotation strategies and provides an open-source data-management environment for research and education in bioinformatics.  ...  Three aspects of EST annotation are automated: 1) searching local or remote biological databases for sequence similarities using Blast services, 2) predicting protein coding sequence from EST data and,  ...  Acknowledgements The authors would like to thank Torsten Seemann for expert advise, Marc Liyanage for providing the MacOSX Apache/PHP/Mysql package http:// www.entropy.ch, the Apache friends for the Windows  ... 
doi:10.1186/1751-0473-1-2 pmid:17147782 pmcid:PMC1636334 fatcat:7fii5lqpabcfbf4t6fsr2ajdxa

EST pipeline system: detailed and automated EST data processing and mining

Hao Xu, Ling He, Yuanzhong Zhu, Wei Huang, Lijun Fang, Lin Tao, Yuedong Zhu, Lin Cai, Huayong Xu, Liang Zhang, Hong Xu, Yan Zhou
2003 Genomics, Proteomics & Bioinformatics  
in the Excel format from the web interface, saving research efforts from routine data processing for biological rules embedded in the data.  ...  The EST Pipeline System, software developed by Hangzhou Genomics Institute (HGI), can automatically analyze different scalar EST sequences by suitable methods.  ...  Recently, some research groups have published their automated or semi-automated procedures for EST data analysis, such as ESTAP (1 ) , and some other web-based systems (2 ) .  ... 
pmid:15629036 pmcid:PMC5172240 fatcat:clfyppankvgqtcivjocy2rs5p4

EST Pipeline System: Detailed and Automated EST Data Processing and Mining

Hao Xu, Ling He, Yuanzhong Zhu, Wei Huang, Lijun Fang, Lin Tao, Yuedong Zhu, Lin Cai, Huayong Xu, Liang Zhang, Hong Yu, Yan Zhou
2003 Genomics, Proteomics & Bioinformatics  
Recently, some research groups have published their automated or semi-automated procedures for EST data analysis, such as ESTAP (1 ) , and some other web-based systems (2 ) .  ...  The classification could help a lot on the understanding of gene function (Figure 10 ). Conclusion The EST Pipeline System is a highly automatic analysis pipeline for EST projects.  ... 
doi:10.1016/s1672-0229(03)01029-5 fatcat:hcmm6vspuzaahbbfs4tiu5oaka

EST Express: PHP/MySQL based automated annotation of ESTs from expression libraries

Robin P Smith, William J Buchser, Marcus B Lemmon, Jose R Pardinas, John L Bixby, Vance P Lemmon
2008 BMC Bioinformatics  
The emergence of redundant databases such as UniGene and centralized annotation engines such as Entrez Gene has allowed the development of software that can analyze a great number of sequences in a matter  ...  Several biological techniques result in the acquisition of functional sets of cDNAs that must be sequenced and analyzed.  ...  Khuri for critical comments on the manuscript.  ... 
doi:10.1186/1471-2105-9-186 pmid:18402700 pmcid:PMC2322989 fatcat:bcfwozbvjbbixagfi4agm2gdnm

A hitchhiker's guide to expressed sequence tag (EST) analysis

S. H. Nagaraj, R. B. Gasser, S. Ranganathan
2006 Briefings in Bioinformatics  
We propose a road map for EST analysis to accelerate the effective analyses of EST data sets.  ...  We provide an overview of the significance of ESTs in the genomic era, their properties and the applications of ESTs.  ...  Acknowledgements Partial funding from Genetic Technologies Limited and the Australian Research Council (LP0667795), and the award of a Macquarie University research scholarship to S.H.N. is acknowledged  ... 
doi:10.1093/bib/bbl015 pmid:16772268 fatcat:wmumdszmnjalhnw5doqjzicxue

OREST: the online resource for EST analysis

Brigitte Waegele, Thorsten Schmidt, H. Werner Mewes, Andreas Ruepp
2008 Nucleic Acids Research  
OREST was successfully applied for the identification and functional characterization of more than 3000 EST sequences of the common marmoset monkey (Callithrix jacchus) as part of an international collaboration  ...  Mapping against genome sequences recovers additional 13% of EST data, which otherwise would escape further analysis.  ...  ACKNOWLEDGEMENTS Funding to pay the Open Access publication charges for this article was provided by Helmholtz Zentrum Mu¨nchen.  ... 
doi:10.1093/nar/gkn253 pmid:18463135 pmcid:PMC2447738 fatcat:jct5mqmdknhc7niiznrhkrqwkm

PLAN: a web platform for automating high-throughput BLAST searches and for managing and mining results

Ji He, Xinbin Dai, Xuechun Zhao
2007 BMC Bioinformatics  
Advances in sequencing technologies pose challenges for high-throughput analysis of large-scale sequence data.  ...  Sequences and BLAST results are organized in projects, the data publication levels of which are controlled by the registered project owners.  ...  Acknowledgements We would like to thank our colleagues at the Noble Foundation, particularly Drs. Francis Kirigwi, Haidi Tu and Jiangqi Wen for their valuable suggestions on the system, and Drs.  ... 
doi:10.1186/1471-2105-8-53 pmid:17291345 pmcid:PMC1800871 fatcat:ajrcqnqqhbe6dkhgk75ibgloae

ESTs in Plants: Where Are We Heading? [chapter]

Sameera Panchangam, Nalini Mallikarjuna, Prashanth Suravajhala
2014 Agricultural Bioinformatics  
Nat Genet 38:31-36 Mao C, Cushman JC, May GD, Weller JW (2003) ESTAP -an automated system for the analysis of EST data.  ...  Some of the recent tools for analysis of EST exclusive to plants are listed out.  ...  As rightly pointed out by many researches, an ideal EST analysis tool should pos sess a few characteristics such as (1) to be fully automated in a pipeline covering all the steps from the input chromatogram  ... 
doi:10.1007/978-81-322-1880-7_9 fatcat:mbegetxcwbf7po7fqcmq3hoewu

In silico analysis of expressed sequence tags from Trichostrongylus vitrinus (Nematoda): comparison of the automated ESTExplorer workflow platform with conventional database searches

Shivashankar H Nagaraj, Robin B Gasser, Alasdair J Nisbet, Shoba Ranganathan
2008 BMC Bioinformatics  
We have recently developed ESTExplorer, a semi-automated computational workflow system, in order to achieve the rapid analysis of EST datasets.  ...  The analysis of expressed sequence tags (EST) offers a rapid and cost effective approach to elucidate the transcriptome of an organism, but requires several computational methods for assembly and annotation  ...  SHN is grateful to Macquarie University for the award of iMURS research scholarships and an MUPGR travel grant. Open Access publication charges for this article were covered by Macquarie University.  ... 
doi:10.1186/1471-2105-9-s1-s10 pmid:18315841 pmcid:PMC2259411 fatcat:u6ak6zmfk5de7jaobvvkfz4ovi

ESTIMA, a tool for EST management in a multi-project environment

Charu G Kumar, Richard LeDuc, George Gong, Levan Roinishivili, Harris A Lewin, Lei Liu
2004 BMC Bioinformatics  
A web application, Expressed Sequence Tag Information Management and Annotation (ESTIMA), has been created to meet the EST annotation and data management requirements of multiple high-throughput EST sequencing  ...  ESTIMA has been used for the management of EST projects of many species, including honeybee (Apis mellifera), cattle (Bos taurus), songbird (Taeniopygia guttata), corn rootworm (Diabrotica vergifera),  ...  We would like to thank the generous support of the Biotechnology Center and W.M.Keck Foundation at the University of Illinois for supporting this work.  ... 
doi:10.1186/1471-2105-5-176 pmid:15527510 pmcid:PMC533868 fatcat:3uslf2bw7ngdpoi7dndk7byy5q

MAGIC-SPP: a database-driven DNA sequence processing package with associated management tools

Chun Liang, Feng Sun, Haiming Wang, Junfeng Qu, Robert M Freeman, Lee H Pratt, Marie-Michèle Cordonnier-Pratt
2006 BMC Bioinformatics  
The database not only serves as a data repository, but also controls processing of trace files.  ...  Processing raw DNA sequence data is an especially challenging task for relatively small laboratories and core facilities that produce as many as 5000 or more DNA sequences per week from multiple projects  ...  Acknowledgements The authors thank Dmitri Kolychev, Zheng Xia, Virgil Edward Johnson and Robert Sullivan for providing valuable assistance.  ... 
doi:10.1186/1471-2105-7-115 pmid:16522212 pmcid:PMC1421442 fatcat:eequtaq4hnbojg3qcyjfcbmreu

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  
Conclusions: The large-scale analysis of relative EST frequency counts among a diverse collection of 23 different cDNA libraries from leaf, berry, and root tissues of wine grape exposed to a variety of  ...  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

A novel approach to sequence validating protein expression clones with automated decision making

Elena Taycher, Andreas Rolfs, Yanhui Hu, Dongmei Zuo, Stephanie E Mohr, Janice Williamson, Joshua LaBaer
2007 BMC Bioinformatics  
Results: We have developed an Automated Clone Evaluation (ACE) system -the first comprehensive, multi-platform, web-based plasmid sequence verification software package.  ...  In a direct comparison, the automated analysis by ACE took less time and was more accurate than a manual analysis of a 93 gene clone set.  ...  Acknowledgements We would like to thank Fontina Kelley, Seamus McCarron, Dan Jepson, Jason Kramer, Yili Li and Ashleigh Ranczuch for their hard work in building and sequencing clones to produce the data  ... 
doi:10.1186/1471-2105-8-198 pmid:17567908 pmcid:PMC1914086 fatcat:ocfblez5o5gjxj5bdv3heahvve
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