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

Bekel, Thomas; Henckel, Kolja; Küster, H.; Meyer, Patrick; Runte, Virginie Mittard; Neuweger, Heiko; Paarmann, Daniel; Rupp, Oliver; Zakrzewski, Martha; Pühler, Alfred; Stoye, Jens; Goesmann, Alexander

doi:10.1016/j.jbiotec.2009.01.006

Cited by 33 publications

(26 citation statements)

References 44 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Data were treated using the "Sequence Analysis and Management System" (SAMS) EST pipeline (Bekel et al, 2009), an open source online pipeline developed by the Center for Biotechnology, Bielefeld University (web site: http://www.cebitec.uni-bielefeld.de/groups/ brf/software/sams_info/).…”

Section: Est Clustering and Annotationmentioning

confidence: 99%

ESTs library from embryonic stages reveals tubulin and reflectin diversity in Sepia officinalis (Mollusca — Cephalopoda)

Bassaglia

Bekel

Silva

et al. 2012

Gene

Self Cite

View full text Add to dashboard Cite

Section: Est Clustering and Annotationmentioning

confidence: 99%

ESTs library from embryonic stages reveals tubulin and reflectin diversity in Sepia officinalis (Mollusca — Cephalopoda)

Bassaglia

Bekel

Silva

et al. 2012

Gene

Self Cite

View full text Add to dashboard Cite

“…A graphical representation of the reference-based transcripts and their intron-exon structures on the CHO-K1 draft genome is publicly available at the GenDBE web-interface [26] (https://gendbe.cebitec.uni-bielefeld.de/cho.html) (Figure 10). Additionally, the final transcripts can be browsed using the SAMS web-interface [27] (https://sams.cebitec.uni-bielefeld.de/cho.html) (Figure 11), which is an extended version of the original SAMS system [28]. A visualization of a possible splicing-graph, representing the splice variants of the cluster, computed from the multiple alignment of the amino-acid sequences using POA [29] and POAVIZ [30], is available for each cluster.…”

Section: Resultsmentioning

confidence: 99%

“…The non-reference-based transcripts were clustered using the wcd clustering tool [40]. The clusters were then uploaded to the SAMS system [28]. The automatic annotation pipeline Metanor-Euk [41] was applied on both data sets with different BLAST [42] searches against various databases, including SwissProt [43], KEGG [44], KOG [45], and eggNOG [46], and HMM based tools such as Pfam [47], InterProScan [48], and Panther [49] for functional prediction.…”

Section: Methodsmentioning

confidence: 99%

Construction of a Public CHO Cell Line Transcript Database Using Versatile Bioinformatics Analysis Pipelines

et al. 2014

Self Cite

View full text Add to dashboard Cite

Chinese hamster ovary (CHO) cell lines represent the most commonly used mammalian expression system for the production of therapeutic proteins. In this context, detailed knowledge of the CHO cell transcriptome might help to improve biotechnological processes conducted by specific cell lines. Nevertheless, very few assembled cDNA sequences of CHO cells were publicly released until recently, which puts a severe limitation on biotechnological research. Two extended annotation systems and web-based tools, one for browsing eukaryotic genomes (GenDBE) and one for viewing eukaryotic transcriptomes (SAMS), were established as the first step towards a publicly usable CHO cell genome/transcriptome analysis platform. This is complemented by the development of a new strategy to assemble the ca. 100 million reads, sequenced from a broad range of diverse transcripts, to a high quality CHO cell transcript set. The cDNA libraries were constructed from different CHO cell lines grown under various culture conditions and sequenced using Roche/454 and Illumina sequencing technologies in addition to sequencing reads from a previous study. Two pipelines to extend and improve the CHO cell line transcripts were established. First, de novo assemblies were carried out with the Trinity and Oases assemblers, using varying k-mer sizes. The resulting contigs were screened for potential CDS using ESTScan. Redundant contigs were filtered out using cd-hit-est. The remaining CDS contigs were re-assembled with CAP3. Second, a reference-based assembly with the TopHat/Cufflinks pipeline was performed, using the recently published draft genome sequence of CHO-K1 as reference. Additionally, the de novo contigs were mapped to the reference genome using GMAP and merged with the Cufflinks assembly using the cuffmerge software. With this approach 28,874 transcripts located on 16,492 gene loci could be assembled. Combining the results of both approaches, 65,561 transcripts were identified for CHO cell lines, which could be clustered by sequence identity into 17,598 gene clusters.

show abstract

“…(b) Comparative genomics is facilitated by EDGAR software [102,103]. Despite being a stand-alone application, it is able to communicate with the well-established genome annotation software GenDB (c) [77], which can be complemented with SAMS for the analysis of shorter DNA sequence data [269]. Specialized tools facilitate the genome-based interpretation of microarray-based transcriptome data (d; EMMA; [129]), proteome data (e; QuPE; [172]), and gas chromatography-mass spectrometry (GC-MS)-based metabolome data (f; MeltDB; [181]).…”

Section: Genomic Basicsmentioning

confidence: 99%

Systems and synthetic biology perspective of the versatile plant-pathogenic and polysaccharide-producing bacterium Xanthomonas campestris

et al. 2017

Self Cite

View full text Add to dashboard Cite

Bacteria of the genus Xanthomonas are a major group of plant pathogens. They are hazardous to important crops and closely related to human pathogens. Being collectively a major focus of molecular phytopathology, an increasing number of diverse and intricate mechanisms are emerging by which they communicate, interfere with host signalling and keep competition at bay. Interestingly, they are also biotechnologically relevant polysaccharide producers. Systems biotechnology techniques have revealed their central metabolism and a growing number of remarkable features. Traditional analyses of Xanthomonas metabolism missed the Embden-Meyerhof-Parnas pathway (glycolysis) as being a route by which energy and molecular building blocks are derived from glucose. As a consequence of the emerging full picture of their metabolism process, xanthomonads were discovered to have three alternative catabolic pathways and they use an unusual and reversible phosphofructokinase as a key enzyme. In this review, we summarize the synthetic and systems biology methods and the bioinformatics tools applied to reconstruct their metabolic network and reveal the dynamic fluxes within their complex carbohydrate metabolism. This is based on insights from omics disciplines; in particular, genomics, transcriptomics, proteomics and metabolomics. Analysis of high-throughput omics data facilitates the reconstruction of organism-specific large-and genome-scale metabolic networks. Reconstructed metabolic networks are fundamental to the formulation of metabolic models that facilitate the simulation of actual metabolic activities under specific environmental conditions. SYSTEMS BIOLOGYIn recent years, systems and synthetic biology have substantially increased our understanding of many processes in life sciences at molecular and cellular levels [1][2][3]. Systems biology intends to understand the cell from a system-wide perspective. For over 100 years, life sciences have aimed at elucidating the details of molecular processes in organisms. In systems biology, scientists have started to inter-relate this data on a large scale in order to analyse the interactions of all elements [4,5], and thus initiate the decoding of entire systems, aiming at their quantitative understanding. This became possible with the development of high-throughput techniques associated with diverse computational methods and the availability of faster computing. Fundamental highthroughput methods are now routinely available in the fields of genomics, transcriptomics, metabolomics and proteomics, while additional specialized branches of omics disciplines have been developed, such as lipidomics [6][7][8], glycomics [9][10][11] and 13 C fluxomics [12,13].

show abstract

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

Cited by 33 publications

References 44 publications

ESTs library from embryonic stages reveals tubulin and reflectin diversity in Sepia officinalis (Mollusca — Cephalopoda)

ESTs library from embryonic stages reveals tubulin and reflectin diversity in Sepia officinalis (Mollusca — Cephalopoda)

Construction of a Public CHO Cell Line Transcript Database Using Versatile Bioinformatics Analysis Pipelines

Systems and synthetic biology perspective of the versatile plant-pathogenic and polysaccharide-producing bacterium Xanthomonas campestris

Contact Info

Product

Resources

About