Bioinformatics Tools and Methods for Plasmid Sequence Analysis and Annotation
Jason R. Grant and Paul Stothard
from: Plasmids: Current Research and Future Trends (Edited by: Georg Lipps). Caister Academic Press, U.K. (2008)
The past decade has seen tremendous growth in the development and application of bioinformatics databases and software. This chapter provides an overview of some of the current bioinformatics tools and methods available for the analysis of plasmid sequences, including resources for obtaining sequences, performing routine analysis operations, and annotating novel sequences. Specific topics covered include sequence databases, restriction analysis, plasmid construction, gene prediction, similarity searches, sequence alignment, annotation pipelines, and visualization tools. In addition, the most popular sequence formats are described, with an emphasis on open formats. Many of the resources presented are applicable to naturally occurring plasmids and to plasmid vectors, from prokaryotic or eukaryotic systems read more ...