We conduct research and resource development in computational biology and bioinformatics. There are analysis resources and links for the biological research community; especially in genome research, genome annotation, gene identification, and protein structure analysis.
http://compbio.ornl.gov/
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Computational Biology at Oak Ridge National Laboratory | compbio.ornl.gov Reviews
https://compbio.ornl.gov
We conduct research and resource development in computational biology and bioinformatics. There are analysis resources and links for the biological research community; especially in genome research, genome annotation, gene identification, and protein structure analysis.
compbio.ornl.gov
Transportation and Directions to Oak Ridge
http://compbio.ornl.gov/new/directions.html
Transportation and Directions to Oak Ridge. Several major airlines have frequent daily flights to the nearby Knoxville McGee Tyson Airport (TYS). Travel from the airport to Oak Ridge takes about 30 minutes via rental car or taxi, available at the airport. ORNL has developed several maps of the area. Directions to the lab from various points of origin are below. Visitors will be issued temporary passes at the guard gate and will be directed to the visitor center. Instructions for "Entering ORNL".
What's New in Computational Biology at ORNL
http://compbio.ornl.gov/new/whatsnew.html
Publications in Comparative Genomics at ORNL
http://compbio.ornl.gov/new/publications.html
Oak Ridge National Laboratory. Post Office Box 2008. Building 1059, Room 203. Oak Ridge, TN 37831-6420. Comparative Genomics at ORNL. BMC Systems Biology 2015, 9:30 doi:10.1186/s12918-015-0159-x. PLoS One. 2015 Jun 2;10(6). Walworth N, Pfreundt U, Nelson WC, Mincer T, Heidelberg JF, Fu FX, Waterbury JB, del Rio TG, Goodwin L, Kyrpides NC, Land ML, Woyke T, Hutchins DA, Hess WR, Webb EA (2015) Trichodesmium genome maintains abundant, widespread noncoding DNA in situ, despite oligotrophic lifestyle. Utturk...
Comparative Genomics at ORNL - Organization Chart
http://compbio.ornl.gov/new/orgchart.html
Oak Ridge National Laboratory. Post Office Box 2008. Building 1059, Room 203. Oak Ridge, TN 37831-6420. Comparative Genomics at ORNL. Ahn, Taehyuk (Ted). Chai, Juanjuan (JJ). Galloway, Leslie D. Galloway, Michael D. Land, Miriam L. Oak Ridge National Laboratory. PO Box 2008, MS 6420. Oak Ridge, TN 37831-6420. June 22, 2015. DOE - Oak Ridge.
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Prodigal: Microbial Gene Prediction Algorithm Description
http://prodigal.ornl.gov/algorithm.html
Prokaryotic Dynamic Programming Genefinding Algorithm. An illustration of the Prodigal dynamic programming connections. Prodigal's algorithm for gene prediction follows the basic principle of KISS. Keep It Simple, Stupid). Compared to other methods, Prodigal's naive log-likelihood functions seem deceptively simple. Despite its lack of complexity (no Hidden Markov Model, no Interpolated Markov Model, etc.), Prodigal nonetheless achieves good results. Constructing a training set for protein coding. A stati...
Prodigal Gene Prediction Results and Comparison with Genbank
http://prodigal.ornl.gov/results.php
Prokaryotic Dynamic Programming Genefinding Algorithm. Evaluating the performance of microbial genefinders is a difficult task, due mainly to the lack of experimentally verified genes in Genbank. A reasonable place to start is the Ecogene. Performance on the Ecogene Verified Gene Set (884 genes, March, 2011). Matching Starts (5' 3'). Is the number of correct genes divided by the number of genes in the Genbank file. "SP", or Specificity. In performing these comparisons, and looking at how other genefindin...
Local Tools, Collaborators, Other Web Sites of Interest
http://dna1.genome.ou.edu/index_pg2.html
Local Tools, Collaborators, Other Web Sites of Interest. Local tools and information. University of Oklahoma ACGT. Human Repeat Sequence Blast Server. Current Time in Norman, Oklahoma, USA. Current Weather Radar for Norman, Oklahoma, USA. National Weather Service (NOAA), Norman, Oklahoma. Current Weather Forcast for Norman, Oklahoma,USA. Satellite Radar for Florida, the Gulf of Mexico and the Caribbean Sea. National Weather Service Hurricane Center - Satellite Imagery. Grantsburg, WI Weather Radar. Inclu...
Abrii Portal > Home
http://www.abrii.ac.ir/en
Monday 22 August 2016. Deputy for Administration and Finance. Tissue Culture and Gene Transformation. Microbial Biotechnology and Biosafety. Northern Region Of Iran-Rasht. West and Northwest Region Of Iran-Tabriz. Northeast and East Region Of Iran-Mashhad. Central Region Of Iran-Esfahan. Research Process Management System. Crop Biotech Update Subscription Form. Iranian Biotechnology Web Sites. National Center for Biotechnology Information (NCBI). European Molecular Biology Laboratory (EMBL).
Brian's List of Some WWW Servers
http://helix.biology.mcmaster.ca/www_servers.html
World Wide Web Servers. If you find some noteable sites/places on the net, mail me a message and I will add them to this page. McMaster (external home page). McMaster (local home page). McMaster Micro Home page. How to build one. ArrayExpress at EBI UK. Microarray at EBI UK. Mouse gene expression at MRC Edinburgh. MAD: a suite of tools for microarray data management and processing. A listing of DNA microarray links. Oasis - Microarray Markup Language (MAML). The ExPASy Molecular Biology Server. Click on ...
Biolinks.html
http://www.molbio.uzh.ch/biolinks/Biolinks.html
BioInformatics links and sites. European Life Sciences Forum ). Amos' WWW links page. National Center for Genome Resources. Abbrev.: L. Hough's list. NAR 29, 1: Molecular Biology Database Collection. The following links return multiple analysis results:. EBI Hinxton - docs. Network Protein Sequence Analysis @PBIL, see also PROSCAN. Protein analysis launcher at SBNet. Pole Bio-Informatique Lyonnais, PBIL. Oligos, Primers, REs,. Find a sequence using keywords. Human Gene Mutation database. List of P lines.
Brian's List of Some WWW Servers
http://helix.mcmaster.ca/www_servers.html
World Wide Web Servers. If you find some noteable sites/places on the net, mail me a message and I will add them to this page. McMaster (external home page). McMaster (local home page). McMaster Micro Home page. How to build one. ArrayExpress at EBI UK. Microarray at EBI UK. Mouse gene expression at MRC Edinburgh. MAD: a suite of tools for microarray data management and processing. A listing of DNA microarray links. Oasis - Microarray Markup Language (MAML). The ExPASy Molecular Biology Server. Click on ...
Prodigal Downloads: Gene Predictions for All of Microbial Genbank
http://prodigal.ornl.gov/downloads.php
Prokaryotic Dynamic Programming Genefinding Algorithm. The latest versions of Prodigal (from 2.6 onward) are available at the Prodigal github page. Old versions of Prodigal:. Prodigal.v2 50.tar.gz. Prodigal.v2 00.tar.gz. Prodigal.v1 20.tar.gz. In addition, Prodigal has been run on all the completed microbial genomes in Genbank. These results are available below. Prodigal Analysis of Completed Microbial Genomes (March, 2011). Acetobacter pasteurianus IFO 3283-01. Acetobacter pasteurianus IFO 3283-01-42C.
Prodigal Bacterial Gene Prediction Server
http://prodigal.ornl.gov/server.html
Prokaryotic Dynamic Programming Genefinding Algorithm. Prodigal v1.20 Analysis Server. Upload your FASTA sequence(s) from file:. Or copy and paste your FASTA sequence(s):. Treat N's as masked RNA genes:. No (Allow gene models to cross gaps). Yes (do not model across large gap of N's). Allow Genes to Run Off Edges:. Gene Coordinates with Protein Translations. Gene Coordinates with Detailed Start Info. Gene Coordinates, Protein Translations, and Detailed Start Info.
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CompBio @ Massey University
These are webpages dedicated to computational biology and related deciplines at the Institute of Natural and Mathematical Sciences (INMS). In Albany, Auckland. The webpages are used to host information and news regarding people, courses, workshops, and conferences as well as research related tools and databases. Building 14, INMS. Station Crescent, Gate 4. Auckland, New Zealand. 64 9 414 0800 (ext: 43538). Gate 4, Building 11, INMS. Auckland 0630, New Zealand.
Computational Genomics (PI: Peter J Park)
We are a bioinformatics research group and are part of the Center for Biomedical Informatics. At Harvard Medical School. Children's Hospital Informatics Program. Harvard-MIT Division of Health, Science, and Technology. And Division of Genetics at Brigham and Women's Hospital. More information on the principal investigator is here. Sep 1, 2014: Not a bad week for the Park lab: we had papers in. All in the same week! Oct 31, 2013: This time, congratulations to Francesco, Andrew! Davis et al. (pp. 3...Recen...
Krawetz Lab
Charlotte B. Failing Professor of Fetal Therapy and Diagnosis. Associate Director C.S. Mott Center for Human Growth and Development,. Wayne State University School of Medicine. Department of Obstetrics and Gynecology. Center for Molecular Medicine and Genetics. Postdoctoral Positions Available - click here. C, Goodrich, R., Swanson, S., Hauser, R., Diamond, M. Click for Full Text. Johnson, G.D., Mackie. SA (2015 Jun 13. pii. Gkv591. [ Epub. Click for Full Text. Analysis methods to examine gene expression...
Compbio.mit.edu - MIT Computational Biology Group - Kellis Lab at MIT and Broad Institute
We work in a highly interdisciplinary environment at the interface of computer science and biology. Members of the group come from a primarily computational background and share a strong passion for understanding biological systems. We are engaged in several collaborative research partnerships with biological and experimental collaborators, at the Broad Institute, the ENCODE, modENCODE, GTEx, and Epigenomics Roadmap consortia, the Harvard Medical School, and other universities. Read more on: Chromatin.
Computational Biology at Oak Ridge National Laboratory
Welcome to Our Web Site. We are the Comparative Genomics and the Computational Biology and Bioinformatics Groups of the Biosciences Division of Oak Ridge National Laboratory. We conduct genetics research and system development in genomic sequencing, computational genome analysis, and computational protein structure analysis. Our collaborators include ORNL's Computer Science and Mathematics Division, the Joint Institute for Biological Sciences, and ORNL's Genome Science and Technology Graduate Program.
CBRG, Oxford University
You are here: CBRG home. Search CBRG web site. Welcome to the CBRG. The Computational Biology Research Group (CBRG) provides computing support. For bioinformatics analysis at the University of Oxford. We have expertise in many aspects of bioinformatics (sequence analysis, microarrays, proteomics and integration). We especially encourage collaborations that require writing custom software, bioinformatics tools and databases. An account with the CBRG has many benefits. Bioinformatics analysis tools online:.
Lab of Computational Biology and Biomolecular Engineering
Lab of Computational Biology and Biomolecular Engineering. 502-203 Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea.
Computational Systems Biology
Please login to view:. If you would like to login and you do not already have an account please contact csb@soihub.org. Acknowledgements: This work was supported by NSF Grant DBI 0835677 and by the Center for Science of Information.
NetCSSP.
Neural networks for calculating Contact-dependent Secondary Structure Propensity. Applications in predicting non-native secondary structures and amyloid fibril formation. 1 Select a method for CSSP calculation. Single network provides helical and beta propensity in a single profile while dual mode calculates the helical and. Beta propensities in two separate neural networks. Three ways to submit a query sequence. 2-1 Paste your protein sequence. PDB ID (4 letters) :. Type sequence (Single letter) :.
Computational Biology Group - Stanford Computer Science Dept
Apply for the Computer Science Ph.D. program. Deadline: Winter 2014. Because of the colleagues, opportunities, facilities, and the true interdisciplinary and entrepreneurial spirit on campus (as well as unmatched weather and Bay Area setting). US News ranks Stanford University as the #1 Best Graduate School in both computer science, biological sciences, and in genetics, genomics and bioinformatics. Stanford Computer Science Department. Related Graduate Programs and Departments.
