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

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. Willi 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 set up, SAMS automatically recognizes the data type. (C) 2009 Elsevier B.V. All rights reserved.