MOTIVATION: Sequence repositories have few well-annotated virus mature peptide sequences. Therefore post-translational proteolytic processing of polyproteins into mature peptides (MPs) has been performed in silico, with a new computational method, for over 200 species in 5 pathogenic virus families (Caliciviridae, Coronaviridae, Flaviviridae, Picornaviridae and Togaviridae). RESULTS: Using pairwise alignment with reference sequences, MPs have been annotated and their sequences made available for search, analysis and download. At publication the method had produced 156 216 sequences, a large portion of the protein sequences now available in https://www.viprbrc.org. It represents a new and comprehensive mature peptide collection. AVAILABILITY AND IMPLEMENTATION: The data are available at the Virus Pathogen Resource https://www.viprbrc.org, and the software at https://github.com/VirusBRC/vipr_mat_peptide.
MOTIVATION: Sequence repositories have few well-annotated virus mature peptide sequences. Therefore post-translational proteolytic processing of polyproteins into mature peptides (MPs) has been performed in silico, with a new computational method, for over 200 species in 5 pathogenic virus families (Caliciviridae, Coronaviridae, Flaviviridae, Picornaviridae and Togaviridae). RESULTS: Using pairwise alignment with reference sequences, MPs have been annotated and their sequences made available for search, analysis and download. At publication the method had produced 156 216 sequences, a large portion of the protein sequences now available in https://www.viprbrc.org. It represents a new and comprehensive mature peptide collection. AVAILABILITY AND IMPLEMENTATION: The data are available at the Virus Pathogen Resource https://www.viprbrc.org, and the software at https://github.com/VirusBRC/vipr_mat_peptide.
Authors: Jason E Stajich; David Block; Kris Boulez; Steven E Brenner; Stephen A Chervitz; Chris Dagdigian; Georg Fuellen; James G R Gilbert; Ian Korf; Hilmar Lapp; Heikki Lehväslaiho; Chad Matsalla; Chris J Mungall; Brian I Osborne; Matthew R Pocock; Peter Schattner; Martin Senger; Lincoln D Stein; Elia Stupka; Mark D Wilkinson; Ewan Birney Journal: Genome Res Date: 2002-10 Impact factor: 9.043
Authors: Brett E Pickett; Eva L Sadat; Yun Zhang; Jyothi M Noronha; R Burke Squires; Victoria Hunt; Mengya Liu; Sanjeev Kumar; Sam Zaremba; Zhiping Gu; Liwei Zhou; Christopher N Larson; Jonathan Dietrich; Edward B Klem; Richard H Scheuermann Journal: Nucleic Acids Res Date: 2011-10-17 Impact factor: 16.971
Authors: Dennis A Benson; Ilene Karsch-Mizrachi; David J Lipman; James Ostell; David L Wheeler Journal: Nucleic Acids Res Date: 2005-01-01 Impact factor: 16.971
Authors: Guangyu Sun; Christopher N Larsen; Nicole Baumgarth; Edward B Klem; Richard H Scheuermann Journal: PLoS One Date: 2017-01-26 Impact factor: 3.240
Authors: Nuala A O'Leary; Mathew W Wright; J Rodney Brister; Stacy Ciufo; Diana Haddad; Rich McVeigh; Bhanu Rajput; Barbara Robbertse; Brian Smith-White; Danso Ako-Adjei; Alexander Astashyn; Azat Badretdin; Yiming Bao; Olga Blinkova; Vyacheslav Brover; Vyacheslav Chetvernin; Jinna Choi; Eric Cox; Olga Ermolaeva; Catherine M Farrell; Tamara Goldfarb; Tripti Gupta; Daniel Haft; Eneida Hatcher; Wratko Hlavina; Vinita S Joardar; Vamsi K Kodali; Wenjun Li; Donna Maglott; Patrick Masterson; Kelly M McGarvey; Michael R Murphy; Kathleen O'Neill; Shashikant Pujar; Sanjida H Rangwala; Daniel Rausch; Lillian D Riddick; Conrad Schoch; Andrei Shkeda; Susan S Storz; Hanzhen Sun; Francoise Thibaud-Nissen; Igor Tolstoy; Raymond E Tully; Anjana R Vatsan; Craig Wallin; David Webb; Wendy Wu; Melissa J Landrum; Avi Kimchi; Tatiana Tatusova; Michael DiCuccio; Paul Kitts; Terence D Murphy; Kim D Pruitt Journal: Nucleic Acids Res Date: 2015-11-08 Impact factor: 16.971