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  1. 2321
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    KinImmerse: Macromolecular VR for NMR ensembles
  2. 2322
    “…Availability: Python and C source code are available upon request from the authors. …”
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    Modeling peptide fragmentation with dynamic Bayesian networks for peptide identification
  3. 2323
    “…Available through a web interface and as downloadable source code, it allows to study positions and to search for motifs inside the whole sequence or within a specified range. …”
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    Entropic Profiler – detection of conservation in genomes using information theory
  4. 2324
    “…We have integrated this annotation pipeline into Gemma. Availability: The source code, documentation and Supplementary Materials are available at http://www.chibi.ubc.ca/GEOMMTX. …”
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    Application and evaluation of automated semantic annotation of gene expression experiments
  5. 2325
    “…RESULTS: Fpocket is an open source pocket detection package based on Voronoi tessellation and alpha spheres built on top of the publicly available package Qhull. The modular source code is organised around a central library of functions, a basis for three main programs: (i) Fpocket, to perform pocket identification, (ii) Tpocket, to organise pocket detection benchmarking on a set of known protein-ligand complexes, and (iii) Dpocket, to collect pocket descriptor values on a set of proteins. …”
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    Fpocket: An open source platform for ligand pocket detection
  6. 2326
    por Nugent, Timothy, Jones, David T
    Publicado 2009
    “…We present the results of applying these tools to a number of complete genomes. Source code, data sets and a web server are freely available from . …”
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    Transmembrane protein topology prediction using support vector machines
  7. 2327
    “…Availability: Contact authors for source code. Contact: brd+ismb08@cs.duke.edu…”
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    Algorithm for backrub motions in protein design
  8. 2328
    “…Availability: MiRank is programmed in Matlab on Windows platform. The source code is available upon request. Contact: zhang@cse.wustl.edu…”
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    MicroRNA prediction with a novel ranking algorithm based on random walks
  9. 2329
    “…Availability: Software to perform the calculation for pairs of position frequency matrices (PFMs) is available at http://mosta.molgen.mpg.de as well as C++ source code for downloading. Contact: utz.pape@molgen.mpg.de…”
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    Statistical detection of cooperative transcription factors with similarity adjustment
  10. 2330
    “…All results are available at CONCLUSION: CASSIOPE makes it possible to study conserved regions from a chosen query genetic region and to infer conserved gene clusters based on phylogenies and statistical tests assessing the significance of these conserved regions. Source code is freely available, please contact: Pierre.pontarotti@univ-provence.fr…”
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    CASSIOPE: An expert system for conserved regions searches
  11. 2331
    “…In general, our approach enables the identification of both cis- and trans-acting ncRNAs in partially or completely sequenced microbial genomes without requiring homology or structural conservation. Availability: The source code and results are available at http://csbl.bmb.uga.edu/publications/materials/tran/. …”
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    De novo computational prediction of non-coding RNA genes in prokaryotic genomes
  12. 2332
    “…CONCLUSION: Evaluations on both real and simulation datasets suggest that BOAT is capable of mapping large volumes of short reads to reference sequences with better sensitivity and lower memory requirement than other currently existing algorithms. The source code and pre-compiled binary packages of BOAT are publicly available for download at http://boat.cbi.pku.edu.cn under GNU Public License (GPL). …”
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    BOAT: Basic Oligonucleotide Alignment Tool
  13. 2333
    “…More information and the source code are available from http://cbe.ipk-gatersleben.de. …”
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    Fast multi-core based multimodal registration of 2D cross-sections and 3D datasets
  14. 2334
    por Wu, Thomas D., Nacu, Serban
    Publicado 2010
    “…Simulations of bisulfite-converted DNA show a decrease in identifying genomic positions uniquely in 6% of 36 nt reads and 3% of 70 nt reads. Availability: Source code in C and utility programs in Perl are freely available for download as part of the GMAP package at http://share.gene.com/gmap. …”
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    Fast and SNP-tolerant detection of complex variants and splicing in short reads
  15. 2335
    por Jiang, Peng, Singh, Mona
    Publicado 2010
    “…Finally, we demonstrate the power of our fast network clustering algorithm by applying SPICi across hundreds of large context-specific human networks, and identifying modules specific for single conditions. Availability: Source code is available under the GNU Public License at http://compbio.cs.princeton.edu/spici Contact: mona@cs.princeton.edu Supplementary information: Supplementary data are available at Bioinformatics online.…”
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    SPICi: a fast clustering algorithm for large biological networks
  16. 2336
    “…Our improvement is especially clear in low identity range of sequences. The source code is available at our web page, whose address is found in the section "Availability and requirements".…”
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    MTRAP: Pairwise sequence alignment algorithm by a new measure based on transition probability between two consecutive pairs of residues
  17. 2337
    “…Availability: The implementation is provided as a freely accessible web application at: http://projects.dbbe.musc.edu/gosteiner. Additionally, the source code written in the Python programming language, is available under the General Public License of the Free Software Foundation. …”
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    Assessing the functional coherence of gene sets with metrics based on the Gene Ontology graph
  18. 2338
    “…Availability and implementation: C++ source code freely available for download at ftp.ncbi.nih.gov/pub/wolf/COGs/COGsoft/ Contact: dmk@stowers.org Supplementary information: Supplementary materials are available at Bioinformatics online.…”
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    A low-polynomial algorithm for assembling clusters of orthologous groups from intergenomic symmetric best matches
  19. 2339
    “…Availability: Documentation, source code and manuals are available at http://genapha.icapture.ubc.ca/SLIMS/index.jsp. …”
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    SLIMS—a user-friendly sample operations and inventory management system for genotyping labs
  20. 2340
    “…High-performance implementations are provided for Unix pipeline integration along with a GUI version for interactive use. Source code in C++ and Java is provided, as are native binaries for Linux, Mac OS X and Windows systems.…”
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    PeakAnalyzer: Genome-wide annotation of chromatin binding and modification loci
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