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2961Protein structure quality assessment based on the distance profiles of consecutive backbone Cα atomspor Chakraborty, Sandeep, Venkatramani, Ravindra, Rao, Basuthkar J., Asgeirsson, Bjarni, Dandekar, Abhaya M.“…This highlights the physical non-viability of the fisa decoy set, and possible issues in benchmarking other methods using this set. The source code and manual is made available at https://github.com/sanchak/mqap and permanently available on 10.5281/zenodo.7134.…”
Publicado 2013
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2962por Milone, Diego H, Stegmayer, Georgina, López, Mariana, Kamenetzky, Laura, Carrari, Fernando“…The algorithm is available as a web-demo at http://fich.unl.edu.ar/sinc/web-demo/bsom-lite/. The source code and the data sets supporting the results of this article are available at http://sourceforge.net/projects/sourcesinc/files/bsom.…”
Publicado 2014
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2963“…CONCLUSION: SMOQ is a useful tool for protein single model quality assessment. Its source code and executable are available at: http://sysbio.rnet.missouri.edu/multicom_toolbox/.…”
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2964“…Another advantage of our methods arises from the explicit feature space representation, which can be used to analyze the characteristic features of protein families. The source code of SVM-DT and SVM-DR is available at http://bioinformatics.hitsz.edu.cn/DistanceSVM/index.jsp…”
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2965“…We also validate the novelty of predictions by evaluating the method on recently reported OMIM associations and on associations recently reported in the literature. Availability: Source code and datasets can be downloaded from http://bigdata.ices.utexas.edu/project/gene-disease. …”
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2966“…Availability: Our software is available and distributed open-source under the GNU Lesser General License Version 2.1 (GNU, February 1999). The source code can be downloaded from http://www.cs.duke.edu/donaldlab/osprey.php or http://iiis.tsinghua.edu.cn/∼compbio/software.html. …”
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2967por Cao, Mengfei, Pietras, Christopher M., Feng, Xian, Doroschak, Kathryn J., Schaffner, Thomas, Park, Jisoo, Zhang, Hao, Cowen, Lenore J., Hescott, Benjamin J.“…The superior performance of capDSD in this context confirms that treating the pathways as probabilistic units is more powerful than simply incorporating pathway edges independently into the network. Availability: All source code for calculating the confidences, for extracting pathway information from KEGG XML files, and for calculating the cDSD, caDSD and capDSD matrices are available from http://dsd.cs.tufts.edu/capdsd Contact: lenore.cowen@tufts.edu or benjamin.hescott@tufts.edu Supplementary information: Supplementary data are available at Bioinformatics online.…”
Publicado 2014
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2968
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2969“…The input data, final results and the source code are available at ftp://ftp.ncbi.nlm.nih.gov/pub/qmbpmn/ProteinComplexDAG/.…”
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2970por Reid, Ian, O’Toole, Nicholas, Zabaneh, Omar, Nourzadeh, Reza, Dahdouli, Mahmoud, Abdellateef, Mostafa, Gordon, Paul MK, Soh, Jung, Butler, Gregory, Sensen, Christoph W, Tsang, Adrian“…CONCLUSIONS: SnowyOwl efficiently uses RNA-Seq data to produce accurate gene models in both well-studied and novel fungal genomes. The source code for the SnowyOwl pipeline (in Python) and a web interface (in PHP) is freely available from http://sourceforge.net/projects/snowyowl/.…”
Publicado 2014
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2971por Söderholm, Sandra, Hintsanen, Petteri, Öhman, Tiina, Aittokallio, Tero, Nyman, Tuula A“…Due to its flexible interface and open source distribution, the users can easily incorporate the program into their MS data analysis workflows and extend the program with new features. PhosFox source code, implementation and user instructions are freely available from https://bitbucket.org/phintsan/phosfox. …”
Publicado 2014
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2972por Wagner, Ines, Volkmer, Michael, Sharan, Malvika, Villaveces, Jose M, Oswald, Felix, Surendranath, Vineeth, Habermann, Bianca H“…CONCLUSIONS: Based on our results, we conclude that morFeus is a powerful and specific search method for detecting remotely conserved orthologs. morFeus is freely available at http://bio.biochem.mpg.de/morfeus/. Its source code is available from Sourceforge.net (https://sourceforge.net/p/morfeus/). …”
Publicado 2014
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2973“…Availability and implementation: Source code is available at www.kostkalab.net/software. …”
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2974por Khan, Suleiman A., Virtanen, Seppo, Kallioniemi, Olli P., Wennerberg, Krister, Poso, Antti, Kaski, Samuel“…Availability and implementation: Source Code implementing the method is available at: http://research.ics.aalto.fi/mi/software/GFAsparse Contact: suleiman.khan@aalto.fi or samuel.kaski@aalto.fi Supplementary Information: Supplementary data are available at Bioinformatics online.…”
Publicado 2014
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2975por Amarasinghe, Kaushalya C, Li, Jason, Hunter, Sally M, Ryland, Georgina L, Cowin, Prue A, Campbell, Ian G, Halgamuge, Saman K“…ADTEx is implemented as a user friendly software package using Python and R statistical language. Source code and sample data are freely available under GNU license (GPLv3) at http://adtex.sourceforge.net/. …”
Publicado 2014
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2976por Tang, Xiaojia, Baheti, Saurabh, Shameer, Khader, Thompson, Kevin J., Wills, Quin, Niu, Nifang, Holcomb, Ilona N., Boutet, Stephane C., Ramakrishnan, Ramesh, Kachergus, Jennifer M., Kocher, Jean-Pierre A., Weinshilboum, Richard M., Wang, Liewei, Thompson, E. Aubrey, Kalari, Krishna R.“…Further, Sanger sequencing validation was performed for an ER+ breast tumor with paired normal adjacent tissue validating 29 out of 31 candidate eSNVs. The source code and user manuals of the eSNV-Detect pipeline for Sun Grid Engine and virtual machine are available at http://bioinformaticstools.mayo.edu/research/esnv-detect/.…”
Publicado 2014
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2977“…The Bio3D package is distributed with full source code and extensive documentation as a platform independent R package under a GPL2 license from http://thegrantlab.org/bio3d/. …”
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2978por Rastegar-Mojarad, Majid, Kadolph, Christopher, Ye, Zhan, Wall, Daniel, Murali, Narayana, Lin, Simon“…CONCLUSIONS: We designed, created a reference implementation, and evaluated a fuzzy-match search engine for physician directories. The open-source code is available at the codeplex website and a reference implementation is available for demonstration at the datamarsh website.…”
Publicado 2014
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2979por Gavrielides, Mike, Furney, Simon J, Yates, Tim, Miller, Crispin J, Marais, RichardEnlace del recurso
Publicado 2014
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2980“…Experimental results, using real and synthetic data, show that this implementation outperforms the one by Pinho et al. The open-source code of our implementation is freely available at http://github.com/solonas13/maw. …”
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