Details
| Original language | English |
|---|---|
| Pages (from-to) | 3-12 |
| Number of pages | 10 |
| Journal | Journal of biotechnology |
| Volume | 140 |
| Issue number | 1-2 |
| Publication status | Published - 10 Mar 2009 |
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.
Keywords
- cDNA sequencing, DNA sequence quality control, EST clustering, Ultrafast sequencing, Whole genome shotgun sequencing
ASJC Scopus subject areas
- Biochemistry, Genetics and Molecular Biology(all)
- Biotechnology
- Chemical Engineering(all)
- Bioengineering
- Immunology and Microbiology(all)
- Applied Microbiology and Biotechnology
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In: Journal of biotechnology, Vol. 140, No. 1-2, 10.03.2009, p. 3-12.
Research output: Contribution to journal › Article › Research › peer review
}
TY - JOUR
T1 - The Sequence Analysis and Management System - SAMS-2.0
T2 - Data management and sequence analysis adapted to changing requirements from traditional sanger sequencing to ultrafast sequencing technologies
AU - Bekel, Thomas
AU - Henckel, Kolja
AU - Küster, Helge
AU - Meyer, Folker
AU - Mittard Runte, Virginie
AU - Neuweger, Heiko
AU - Paarmann, Daniel
AU - Rupp, Oliver
AU - Zakrzewski, Martha
AU - Pühler, Alfred
AU - Stoye, Jens
AU - Goesmann, Alexander
N1 - Funding information: TB acknowledges financial support from Degussa GmbH and the Bundesministerium für Bildung und Forschung (BMBF), SysMAP project (grant 0313704). KH and HN would like to thank the International Graduate School in Bioinformatics and Genome Research for providing financial support. VMR and MZ received financial support from the EU Excellence Network of Marine Genomics.
PY - 2009/3/10
Y1 - 2009/3/10
N2 - 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.
AB - 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.
KW - cDNA sequencing
KW - DNA sequence quality control
KW - EST clustering
KW - Ultrafast sequencing
KW - Whole genome shotgun sequencing
UR - http://www.scopus.com/inward/record.url?scp=61649088083&partnerID=8YFLogxK
U2 - 10.1016/j.jbiotec.2009.01.006
DO - 10.1016/j.jbiotec.2009.01.006
M3 - Article
C2 - 19297685
AN - SCOPUS:61649088083
VL - 140
SP - 3
EP - 12
JO - Journal of biotechnology
JF - Journal of biotechnology
SN - 0168-1656
IS - 1-2
ER -