TimeLogic,
Biocomputing Solutions
Applications

Genome Annotation

TimeLogic's DeCypher® systems are ideal for genomics specialists that create tools for data exploration and discovery and maintain genome-specific data portals. Our low form-factor FPGA-accelerated solutions free bioinformaticians from having to rely heavily on IT support. In a single cluster node or desktop workstation, comprehensive BLAST, Smith-Waterman, and gene modeling analyses can be run against well-curated databases of known nucleic or protein sequences. Protein sequences can also be compared to to annotated Hidden Markov Model databases such as PFAM. Additionally, the HMM-Framesearch method is available for automatic translation of your nucleic sequences and frameshift tolerant alignments while assigning protein families.

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Related Scientific Citations

Below is a short list of some recent DeCypher citations for Genome Annotation. For the complete list, please vist our citations page here.

  1. Comparative genomics of citric-acid-producing Aspergillus niger ATCC 1015 versus enzyme-producing CBS 513.88
    Andersen MR, Salazar MP, Schaap PJ, van de Vondervoort PJ, Culley D, Thykaer J, Frisvad JC, Nielsen KF, Albang R, Albermann K, Berka RM, Braus GH, Braus-Stromeyer SA, Corrochano LM, Dai Z, van Dijck PW, Hofmann G, Lasure LL, Magnuson JK, Menke H, Meijer M, Meijer SL, Nielsen JB, Nielsen ML, van Ooyen AJ, Pel HJ, Poulsen L, Samson RA, Stam H, Tsang A, van den Brink JM, Atkins A, Aerts A, Shapiro H, Pangilinan J, Salamov A, Lou Y, Lindquist E, Lucas S, Grimwood J, Grigoriev IV, Kubicek CP, Martinez D, van Peij NN, Roubos JA, Nielsen J, Baker SE.
    Genome Res. 2011 Jun;21(6):885-97.
  2. Finished Genome of the Fungal Wheat Pathogen Mycosphaerella graminicola Reveals Dispensome Structure, Chromosome Plasticity, and Stealth Pathogenesis
    Stephen B. Goodwin, Sarrah Ben M'Barek, Braham Dhillon, Alexander H. J. Wittenberg, Charles F. Crane, James K. Hane, Andrew J. Foster, Theo A. J. Van der Lee, Jane Grimwood, Andrea Aerts, John Antoniw, Andy Bailey, Burt Bluhm, Judith Bowler, Jim Bristow, Ate van der Burgt, Blondy Canto-Canché, Alice C. L. Churchill, Laura Conde-Ferràez, Hans J. Cools, Pedro M. Coutinho, Michael Csukai, Paramvir Dehal, Pierre De Wit, Bruno Donzelli, Henri C. van de Geest, Roeland C. H. J. van Ham, Kim E. Hammond-Kosack, Bernard Henrissat, Andrzej Kilian, Adilson K. Kobayashi, Edda Koopmann, Yiannis Kourmpetis, Arnold Kuzniar, Erika Lindquist, Vincent Lombard, Chris Maliepaard, Natalia Martins, Rahim Mehrabi, Jan P. H. Nap, Alisa Ponomarenko, Jason J. Rudd, Asaf Salamov, Jeremy Schmutz, Henk J. Schouten, Harris Shapiro, Ioannis Stergiopoulos, Stefano F. F. Torriani, Hank Tu, Ronald P. de Vries, Cees Waalwijk, Sarah B. Ware, Ad Wiebenga, Lute-Harm Zwiers, Richard P. Oliver, Igor V. Grigoriev, Gert H. J. Kema.
    PLoS Genet 7(6): e1002070.
  3. Niche of harmful alga Aureococcus anophagefferens revealed through ecogenomics
    Christopher Gobler, Dianna Berry, Sonya Dyhrman, and Steven Wilhelm.
    Proceedings of the National Academy of Sciences of the USA 108.11 (2011): 4352-4357.
  4. Development and Application of Bovine and Porcine Oligonucleotide Arrays with Protein-Based Annotation.
    John R. Garbe, Christine G. Elsik, Eric Antoniou, et al.
    Journal of Biomedicine and Biotechnology, vol. 2010, Article ID 453638, 11 pages.
  5. A Brassica Exon Array for Whole-Transcript Gene Expression Profiling
    Christopher G. Love, Neil S. Graham, Seosamh Ó Lochlainn, Helen C. Bowen4, Sean T. May, Philip J. White, Martin R. Broadley, John P. Hammond, Graham J. King
    PLoS ONE (2010), 5(9): e12812.