Francesco Marass1, Chris Upton. 1. Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 3P6, Canada. fmarass@uvic.ca
Abstract
BACKGROUND: Many sequence-searching tools have limiting factors for their use. For example, they may be platform specific, enforce restrictive size limits and sequences to be searched, or only allow searches of one of DNA or protein. FINDINGS: We present an easy-to-use, fast, platform-independent tool to search for amino acid or nucleotide patterns within one or many protein or nucleic acid sequences. The user can choose to search for regular expressions or perform a fuzzy search in which a particular number of errors is accepted during matching of a sequence. Positions of mismatches in fuzzy searches are displayed graphically the user. CONCLUSION: SeqS provides an improved feature set and functions as a stand-alone tool or could be integrated into other bioinformatics platforms.
BACKGROUND: Many sequence-searching tools have limiting factors for their use. For example, they may be platform specific, enforce restrictive size limits and sequences to be searched, or only allow searches of one of DNA or protein. FINDINGS: We present an easy-to-use, fast, platform-independent tool to search for amino acid or nucleotide patterns within one or many protein or nucleic acid sequences. The user can choose to search for regular expressions or perform a fuzzy search in which a particular number of errors is accepted during matching of a sequence. Positions of mismatches in fuzzy searches are displayed graphically the user. CONCLUSION: SeqS provides an improved feature set and functions as a stand-alone tool or could be integrated into other bioinformatics platforms.
Authors: Christian J A Sigrist; Lorenzo Cerutti; Nicolas Hulo; Alexandre Gattiker; Laurent Falquet; Marco Pagni; Amos Bairoch; Philipp Bucher Journal: Brief Bioinform Date: 2002-09 Impact factor: 11.622
Authors: Brad R Rosenberg; Claire E Hamilton; Michael M Mwangi; Scott Dewell; F Nina Papavasiliou Journal: Nat Struct Mol Biol Date: 2011-01-23 Impact factor: 15.369
Authors: Metehan Cifdaloz; Lisa Osterloh; Osvaldo Graña; Erica Riveiro-Falkenbach; Pilar Ximénez-Embún; Javier Muñoz; Cristina Tejedo; Tonantzin G Calvo; Panagiotis Karras; David Olmeda; Belén Miñana; Gonzalo Gómez-López; Estela Cañon; Eduardo Eyras; Haihong Guo; Ferdinand Kappes; Pablo L Ortiz-Romero; Jose L Rodríguez-Peralto; Diego Megías; Juan Valcárcel; María S Soengas Journal: Nat Commun Date: 2017-12-21 Impact factor: 14.919