The Sequence Analysis and Management System - SAMS-2.0

Data management and sequence analysis adapted to changing requirements from traditional sanger sequencing to ultrafast sequencing technologies

authored by: Thomas Bekel, Kolja Henckel, Helge Küster, Folker Meyer, Virginie Mittard Runte, Heiko Neuweger, Daniel Paarmann, Oliver Rupp, Martha Zakrzewski, Alfred Pühler, Jens Stoye, Alexander Goesmann
Abstract: DNA sequencing plays a more and more important role in various fields of genetics. This includes sequencing of whole genomes, libraries of cDNA clones and probes of metagenome communities. The applied sequencing technologies evolve permanently. With the emergence of ultrafast sequencing technologies, a new era of DNA sequencing has recently started. Concurrently, the needs for adapted bioinformatics tools arise. Since the ability to process current datasets efficiently is essential for modern genetics, a modular bioinformatics platform providing extensive sequence analysis methods, is designated to achieve well the constantly growing requirements. The Sequence Analysis and Management System (SAMS) is a bioinformatics software platform with a database backend designed to support the computational analysis of (1) whole genome shotgun (WGS) bacterial genome sequencing, (2) cDNA sequencing by reading expressed sequence tags (ESTs) as well as (3) sequence data obtained by ultrafast sequencing. It provides extensive bioinformatics analysis of sequenced single reads, sequencing libraries and fragments of arbitrary DNA sequences such as assembled contigs of metagenome reads for instance. The system has been implemented to cope with several thousands of sequences, efficiently processing them and storing the results for further analysis. With the project setup, SAMS automatically recognizes the data type.
Organisation(s): Institute of Plant Genetics
External Organisation(s): Bielefeld University
Argonne National Laboratory
Type: Article
Journal: Journal of biotechnology
Volume: 140
Pages: 3-12
No. of pages: 10
ISSN: 0168-1656
Publication date: 10.03.2009
Publication status: Published
Peer reviewed: Yes
ASJC Scopus subject areas: Biotechnology, Bioengineering, Applied Microbiology and Biotechnology
Electronic version(s): https://doi.org/10.1016/j.jbiotec.2009.01.006 (Access: Unknown)