TETRA

TETRA: a web-service and a stand-alone program for the analysis and comparison of tetranucleotide usage patterns in DNA sequences. Background: In the emerging field of environmental genomics, direct cloning and sequencing of genomic fragments from complex microbial communities has proven to be a valuable source of new enzymes, expanding the knowledge of basic biological processes. The central problem of this so called metagenome-approach is that the cloned fragments often lack suitable phylogenetic marker genes, rendering the identification of clones that are likely to originate from the same genome difficult or impossible. In such cases, the analysis of intrinsic DNA-signatures like tetranucleotide frequencies can provide valuable hints on fragment affiliation. With this application in mind, the TETRA web-service and the TETRA stand-alone program have been developed, both of which automate the task of comparative tetranucleotide frequency analysis. Availability: http://www.megx.net/tetra


References in zbMATH (referenced in 12 articles )

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  1. Ostash, Bohdan; Anisimova, Maria: Visualizing codon usage within and across genomes: concepts and tools (2020)
  2. Garbarine, Elaine; DePasquale, Joseph; Gadia, Vinay; Polikar, Robi; Rosen, Gail: Information-theoretic approaches to SVM feature selection for metagenome read classification (2011)
  3. Nalbantoglu, Ozkan U.; Way, Samuel F.; Hinrichs, Steven H.; Sayood, Khalid: Raiphy: phylogenetic classification of metagenomics samples using iterative refinement of relative abundance index profiles (2011) ioport
  4. Yang, Bin; Peng, Yu; Leung, Henry Chi-Ming; Yiu, Siu-Ming; Chen, Jing-Chi; Chin, Francis Yuk-Lun: Unsupervised binning of environmental genomic fragments based on an error robust selection of (l)-mers (2010) ioport
  5. Diaz, Naryttza N.; Krause, Lutz; Goesmann, Alexander; Niehaus, Karsten; Nattkemper, Tim W.: TACOA - taxonomic classification of environmental genomic fragments using a kernelized nearest neighbor approach (2009) ioport
  6. Gerlach, Wolfgang; Jünemann, Sebastian; Tille, Felix; Goesmann, Alexander; Stoye, Jens: Webcarma: a web application for the functional and taxonomic classification of unassembled metagenomic reads (2009) ioport
  7. Kislyuk, Andrey; Bhatnagar, Srijak; Dushoff, Jonathan; Weitz, Joshua S.: Unsupervised statistical clustering of environmental shotgun sequences (2009) ioport
  8. Li, Weizhong: Analysis and comparison of very large metagenomes with fast clustering and functional annotation (2009) ioport
  9. Wooley, John C.; Ye, Yuzhen: Metagenomics: facts and artifacts, and computational challenges (2009) ioport
  10. Rosen, Gail; Garbarine, Elaine; Caseiro, Diamantino; Polikar, Robi; Sokhansanj, Bahrad: Metagenome fragment classification using (N)-mer frequency profiles (2008) ioport
  11. Schloss, Patrick; Handelsman, Jo: A statistical toolbox for metagenomics: Assessing functional diversity in microbial communities (2008) ioport
  12. Teeling, Hanno; Waldmann, Jost; Lombardot, Thierry; Bauer, Margarete; Glockner, Frank O.: TETRA: a web-service and a stand-alone program for the analysis and comparison of tetranucleotide usage patterns in DNA sequences (2004) ioport