MOTIVATION: High accuracy of data always governs the large-scale gene discovery projects. The data should not only be trustworthy but should be correctly annotated for various features it contains. Sequence errors are inherent in single-pass sequences such as ESTs obtained from automated sequencing. These errors further complicate the automated identification of EST-related sequencing. A tool is required to prepare the data prior to advanced annotation processing and submission to public databases. RESULTS: This paper describes ESTprep, a program designed to preprocess expressed sequence tag (EST) sequences. It identifies the location of features present in ESTs and allows the sequence to pass only if it meets various quality criteria. Use of ESTprep has resulted in substantial improvement in accurate EST feature identification and fidelity of results submitted to GenBank. AVAILABILITY: The program is freely available for download from http://genome.uiowa.edu/pubsoft/software.html
MOTIVATION: High accuracy of data always governs the large-scale gene discovery projects. The data should not only be trustworthy but should be correctly annotated for various features it contains. Sequence errors are inherent in single-pass sequences such as ESTs obtained from automated sequencing. These errors further complicate the automated identification of EST-related sequencing. A tool is required to prepare the data prior to advanced annotation processing and submission to public databases. RESULTS: This paper describes ESTprep, a program designed to preprocess expressed sequence tag (EST) sequences. It identifies the location of features present in ESTs and allows the sequence to pass only if it meets various quality criteria. Use of ESTprep has resulted in substantial improvement in accurate EST feature identification and fidelity of results submitted to GenBank. AVAILABILITY: The program is freely available for download from http://genome.uiowa.edu/pubsoft/software.html
Authors: Christopher K Tuggle; Jon A Green; Carolyn Fitzsimmons; Rami Woods; Randall S Prather; Sergei Malchenko; Bento M Soares; Tamara Kucaba; Keith Crouch; Christina Smith; Dylan Tack; Natalie Robinson; Brian O'Leary; Todd Scheetz; Thomas Casavant; Daniel Pomp; Brad J Edeal; Yuandan Zhang; Max F Rothschild; Kevin Garwood; William Beavis Journal: Mamm Genome Date: 2003-08 Impact factor: 2.957
Authors: Juan Falgueras; Antonio J Lara; Noé Fernández-Pozo; Francisco R Cantón; Guillermo Pérez-Trabado; M Gonzalo Claros Journal: BMC Bioinformatics Date: 2010-01-20 Impact factor: 3.169
Authors: Eduardo R Macagno; Terry Gaasterland; Lee Edsall; Vineet Bafna; Marcelo B Soares; Todd Scheetz; Thomas Casavant; Corinne Da Silva; Patrick Wincker; Aurélie Tasiemski; Michel Salzet Journal: BMC Genomics Date: 2010-06-25 Impact factor: 3.969
Authors: Todd E Scheetz; Jennifer J Laffin; Brian Berger; Sara Holte; Susan A Baumes; Robert Brown; Shereen Chang; Justin Coco; Jim Conklin; Keith Crouch; Micca Donohue; Greg Doonan; Chris Estes; Mari Eyestone; Katrina Fishler; Jack Gardiner; Lankai Guo; Brad Johnson; Catherine Keppel; Rikki Kreger; Mark Lebeck; Rudy Marcelino; Vladan Miljkovich; Mindee Perdue; Ling Qui; Joshua Rehmann; Rebecca S Reiter; Bridgette Rhoads; Kelly Schaefer; Christina Smith; Ivana Sunjevaric; Kurtis Trout; Ning Wu; Clayton L Birkett; Jared Bischof; Barry Gackle; Allen Gavin; A Jason Grundstad; Brian Mokrzycki; Chris Moressi; Brian O'Leary; Kevin Pedretti; Chad Roberts; Natalie L Robinson; Michael Smith; Dylan Tack; Nishank Trivedi; Tamara Kucaba; Tom Freeman; Jim J-C Lin; Maria F Bonaldo; Thomas L Casavant; Val C Sheffield; M Bento Soares Journal: Genome Res Date: 2004-04 Impact factor: 9.043
Authors: Carlene K Chun; Todd E Scheetz; Maria de Fatima Bonaldo; Bartley Brown; Anik Clemens; Wendy J Crookes-Goodson; Keith Crouch; Tad DeMartini; Mari Eyestone; Michael S Goodson; Bernadette Janssens; Jennifer L Kimbell; Tanya A Koropatnick; Tamara Kucaba; Christina Smith; Jennifer J Stewart; Deyan Tong; Joshua V Troll; Sarahrose Webster; Jane Winhall-Rice; Cory Yap; Thomas L Casavant; Margaret J McFall-Ngai; M Bento Soares Journal: BMC Genomics Date: 2006-06-16 Impact factor: 3.969
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
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