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ESTAnnotator: a tool for high throughput EST annotation

A. Hotz-Wagenblatt
2003 Nucleic Acids Research  
ESTAnnotator is a tool for the high throughput annotation of expressed sequence tags (ESTs) by automatically running a collection of bioinformatics applications.  ...  Subsequently, tools for the clustering of anonymous ESTs, and for further database searches at the protein level, are applied.  ...  Figure 1 . 1 Program flow in ESTAnnotator. Programs and rules used for high throughput annotation of ESTs.  ... 
doi:10.1093/nar/gkg566 pmid:12824401 pmcid:PMC169160 fatcat:apx5g4a5ajhehaduuvwgfcjtxu

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.  ...  The most appropriate software tools for EST pre-processing, clustering and assembly, database matching and functional annotation have been compiled (available online from http://biolinfo.org/EST).  ...  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  
To enable functional analysis of the datasets, ESTs are functionally annotated using the hierarchical FunCat annotation scheme as well as GO annotation terms.  ...  OREST (http://mips.gsf.de/genre/proj/orest/index. html) is a server-based EST analysis pipeline, which allows the rapid analysis of large amounts of ESTs or cDNAs from mammalia and fungi.  ...  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

FastAnnotator--an efficient transcript annotation web tool

Ting-Wen Chen, Ruei-Chi Richie Gan, Timothy H Wu, Po-Jung Huang, Cheng-Yang Lee, Yi-Ywan M Chen, Che-Chun Chen, Petrus Tang
2012 BMC Genomics  
We demonstrated that FastAnnotator can complete the annotation process in a reasonable amount of time and is suitable for the annotation of transcriptomes from model organisms or organisms for which annotated  ...  Recent developments in high-throughput sequencing (HTS) technologies have made it feasible to sequence the complete transcriptomes of non-model organisms or metatranscriptomes from environmental samples  ...  Acknowledgements This work is supported by a grant (CMRPD190142) from the Chang Gung Memorial Hospital to PT. We thank Dr. Frith for his useful suggestion on parsing the output data from LAST.  ... 
doi:10.1186/1471-2164-13-s7-s9 pmid:23281853 pmcid:PMC3521244 fatcat:uqi2zxybafafbmc7n4u5itsynq

GarlicESTdb: an online database and mining tool for garlic EST sequences

Dae-Won Kim, Tae-Sung Jung, Seong-Hyeuk Nam, Hyuk-Ryul Kwon, Aeri Kim, Sung-Hwa Chae, Sang-Haeng Choi, Dong-Wook Kim, Ryong Nam Kim, Hong-Seog Park
2009 BMC Plant Biology  
Description: GarlicESTdb is an integrated database and mining tool for large-scale garlic (Allium sativum) EST sequencing.  ...  For all that, there are no comprehensive databases available for Expressed Sequence Tags(EST) of garlic for gene discovery and future efforts of genome annotation.  ...  Acknowledgements We are grateful to the plant biology research community for their valuable input on this project and suggestions in building and maintaining this database.  ... 
doi:10.1186/1471-2229-9-61 pmid:19445732 pmcid:PMC2689220 fatcat:clmj5u7zr5bpnndoraj3mqcsja

E2D: A Novel Tool for Annotating Protein Domains in Expressed Sequence Tags

Guo-Hsing Lee, Nai-Yu Chuang, Wen-Dar Lin, Chung-Der Hsiao, Hahn-Ming Lee, Jan-Ming Ho
2006 2006 IEEE Symposium on Computational Intelligence and Bioinformatics and Computational Biology  
A variety of methods based on homology search or domain profile search have been developed to functionally annotate protein domains in ESTs.  ...  We provide an efficient and novel tool, called E2D (EST to Domain), which functionally annotates anonymous ESTs by recognizing potential domains from the enlarged hit proteins.  ...  Ming-Jing Hwang of the Institute of Biomedical Sciences, Academia Sinica who gave us a great deal of invaluable advice on biology.  ... 
doi:10.1109/cibcb.2006.330967 dblp:conf/cibcb/LeeCLHLH06 fatcat:tg2vkzkvq5dgpgabxdcjxhryoq

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

Sameera Panchangam, Nalini Mallikarjuna, Prashanth Suravajhala
2014 Agricultural Bioinformatics  
J Exp Bot 60 (10):2805-2815. doi:10.1093/jxb/erp211 Hotz-Wagenblatt A, Hankeln T, Ernst P et al (2003) ESTAnnotator: a tool for high throughput EST anno tation.  ...  Plant Biotechnol J 1:141-154 Conesa A, Gotz S, Garcia-Gomez JM et al (2005) Blast2GO: a universal tool for annotation, visualiza tion and analysis in functional genomics research.  ...  In combination with NGS, ESTs have proven to be an extremely valuable resource for high-throughput gene discovery, identification of novel genes, splice variants, gene location, and intron-exon boundaries  ... 
doi:10.1007/978-81-322-1880-7_9 fatcat:mbegetxcwbf7po7fqcmq3hoewu

EST2Prot: mapping EST sequences to proteins

Paul Shafer, David M Lin, Golan Yona
2006 BMC Genomics  
It produces a mapping between ESTs and proteins in real-time through a simple web-interface. The system is part of the Biozon database and is accessible at http://biozon.org/tools/est/.  ...  We describe a system (EST2Prot) that uses multiple elements to map EST sequences to their corresponding protein products.  ...  Acknowledgements We thank Aaron Birkland for his help with the Biozon database.  ... 
doi:10.1186/1471-2164-7-41 pmid:16515706 pmcid:PMC1456965 fatcat:upvwnwcs4rcvzpaqwq2pyeu66q

Advances in Omics Approaches for Abiotic Stress Tolerance in Tomato

Juhi Chaudhary, Praveen Khatri, Pankaj Singla, Surbhi Kumawat, Anu Kumari, Vinaykumar R, Amit Vikram, Salesh Kumar Jindal, Hemant Kardile, Rahul Kumar, Humira Sonah, Rupesh Deshmukh
2019 Biology  
Tomato, one of the most important crops worldwide, has a high demand in the fresh fruit market and processed food industries.  ...  Extensive cataloging of omics resources made here has highlighted the need for integration of omics approaches for efficient utilization of resources and a better understanding of the molecular mechanism  ...  Acknowledgments: Authors are thankful to Department of Biotechnology, Government of India for the Ramalingaswami Fellowship Award to H.S. and R.D., and to University Grants Commission, India for Ph.D.  ... 
doi:10.3390/biology8040090 pmid:31775241 pmcid:PMC6956103 fatcat:mkq4xsb3l5cfhkp33ui77kh6be

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  
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  ...  We further compared the automated EST sequence annotations, using ESTExplorer, with database search results for individual T. vitrinus ESTs.  ...  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

SeqTrim: a high-throughput pipeline for preprocessing any type of sequence reads

Juan Falgueras, Antonio J Lara, Noe Fernandez-Pozo, Francisco R. Canton, Guillermo Perez-Trabado, M. Gonzalo Claros
2010 BMC Bioinformatics  
High-throughput automated sequencing has enabled an exponential growth rate of sequencing data.  ...  Results: SeqTrim has been implemented both as a Web and as a standalone command line application.  ...  Acknowledgements The authors would like to acknowledge Darío Guerrero for his invaluable help concerning Web design and programming advice.  ... 
doi:10.1186/1471-2105-11-38 pmid:20089148 pmcid:PMC2832897 fatcat:2uenosqwl5bznmlyc27fjmrquq

Sma3s: A Three-Step Modular Annotator for Large Sequence Datasets

A. Munoz-Merida, E. Viguera, M. G. Claros, O. Trelles, A. J. Perez-Pulido
2014 DNA Research  
In conclusion, Sma3s is a versatile tool for high-throughput annotation of a wide variety of sequence datasets that outperforms the accuracy of other well-established annotation algorithms, and it can  ...  We present Sma3s, a tool for automatically annotating very large collections of biological sequences from any kind of gene library or genome.  ...  Funding This work has been partially financed by the National Institute for Bioinformatics (www.inab.org), a platform of Genoma España and the EC project 'Advancing Clinico-Genomic Trials on Cancer' (contract  ... 
doi:10.1093/dnares/dsu001 pmid:24501397 pmcid:PMC4131829 fatcat:nh5hntkhu5gjfouxftneb45joy

BIO101-EST sequence management and annotation system

In-Yee Lee, Wen-Chang Lin, Jan-Ming Ho, Gu-Liang Wang, Ming-Syan Chen
Proceedings of the Fifth IEEE International Symposium on Signal Processing and Information Technology, 2005.  
The system includes a) laboratory-based authorization, project-focused and custom database management features; b) a pipeline with integrated tools for producing and clustering highquality ESTs and for  ...  Here we describe BIO101, a centralized approach to laboratory EST sequence management and functional annotation.  ...  s PEDANT [5] , designed for high-throughput analysis of large biological sequence sets, uses manual annotation as a means for refining its automated assignments.  ... 
doi:10.1109/isspit.2005.1577067 fatcat:2yik22sghff4xefmsu7wog5pvm

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.  ...  CONCLUSION High-throughput EST analysis requires integrated and automated approaches enabling EST data mining.  ... 
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  ...  and annotation to yield biologically relevant information.  ...  ACKNOWLEDGEMENTS We are grateful to Macquarie University for the award of postgraduate research scholarships.  ... 
doi:10.25949/19438937 fatcat:kqbdkdfs5bbevk6qfxzg4z5gbi
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