Literature DB >> 12912845

ESTWeb: bioinformatics services for EST sequencing projects.

Apuã C M Paquola1, Milton Y Nishyiama, Eduardo M Reis, Aline M da Silva, Sergio Verjovski-Almeida.   

Abstract

ESTWeb is an internet based software package designed for uniform data processing and storage for large-scale EST sequencing projects. The package provides for: (a) reception of sequencing chromatograms; (b) sequence processing such as base-calling, vector screening, comparison with public databases; (c) storage of data and analysis in a relational database, (d) generation of a graphical report of individual sequence quality; and (e) issuing of reports with statistics of productivity and redundancy. The software facilitates real-time monitoring and evaluation of EST sequence acquisition progress along an EST sequencing project.

Mesh:

Year:  2003        PMID: 12912845     DOI: 10.1093/bioinformatics/btg196

Source DB:  PubMed          Journal:  Bioinformatics        ISSN: 1367-4803            Impact factor:   6.937


  13 in total

1.  Gene discovery and expression profile analysis through sequencing of expressed sequence tags from different developmental stages of the chytridiomycete Blastocladiella emersonii.

Authors:  Karina F Ribichich; Silvia M Salem-Izacc; Raphaela C Georg; Ricardo Z N Vêncio; Luci D Navarro; Suely L Gomes
Journal:  Eukaryot Cell       Date:  2005-02

2.  TranSeqAnnotator: large-scale analysis of transcriptomic data.

Authors:  Ranjeeta Menon; Gagan Garg; Robin B Gasser; Shoba Ranganathan
Journal:  BMC Bioinformatics       Date:  2012-12-13       Impact factor: 3.169

3.  Saci-1, -2, and -3 and Perere, four novel retrotransposons with high transcriptional activities from the human parasite Schistosoma mansoni.

Authors:  Ricardo DeMarco; Andre T Kowaltowski; Abimael A Machado; M Bento Soares; Cybele Gargioni; Toshie Kawano; Vanderlei Rodrigues; Alda M B N Madeira; R Alan Wilson; Carlos F M Menck; João C Setubal; Emmanuel Dias-Neto; Luciana C C Leite; Sergio Verjovski-Almeida
Journal:  J Virol       Date:  2004-03       Impact factor: 5.103

4.  Transcriptome analysis in response to heat shock and cadmium in the aquatic fungus Blastocladiella emersonii.

Authors:  Raphaela C Georg; Suely L Gomes
Journal:  Eukaryot Cell       Date:  2007-04-20

5.  Next generation transcriptomes for next generation genomes using est2assembly.

Authors:  Alexie Papanicolaou; Remo Stierli; Richard H Ffrench-Constant; David G Heckel
Journal:  BMC Bioinformatics       Date:  2009-12-24       Impact factor: 3.169

6.  preAssemble: a tool for automatic sequencer trace data processing.

Authors:  Alexei A Adzhubei; Jon K Laerdahl; Anna V Vlasova
Journal:  BMC Bioinformatics       Date:  2006-01-17       Impact factor: 3.169

7.  JUICE: a data management system that facilitates the analysis of large volumes of information in an EST project workflow.

Authors:  Mariano Latorre; Herman Silva; Juan Saba; Carito Guziolowski; Paula Vizoso; Veronica Martinez; Jonathan Maldonado; Andrea Morales; Rodrigo Caroca; Veronica Cambiazo; Reinaldo Campos-Vargas; Mauricio Gonzalez; Ariel Orellana; Julio Retamales; Lee A Meisel
Journal:  BMC Bioinformatics       Date:  2006-11-23       Impact factor: 3.169

8.  ESTPiper--a web-based analysis pipeline for expressed sequence tags.

Authors:  Zuojian Tang; Jeong-Hyeon Choi; Chris Hemmerich; Ankita Sarangi; John K Colbourne; Qunfeng Dong
Journal:  BMC Genomics       Date:  2009-04-21       Impact factor: 3.969

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

Authors:  Chun Liang; Feng Sun; Haiming Wang; Junfeng Qu; Robert M Freeman; Lee H Pratt; Marie-Michèle Cordonnier-Pratt
Journal:  BMC Bioinformatics       Date:  2006-03-07       Impact factor: 3.169

10.  WebTraceMiner: a web service for processing and mining EST sequence trace files.

Authors:  Chun Liang; Gang Wang; Lin Liu; Guoli Ji; Yuansheng Liu; Jinqiao Chen; Jason S Webb; Greg Reese; Jeffrey F D Dean
Journal:  Nucleic Acids Res       Date:  2007-05-08       Impact factor: 16.971

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