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Perez-Riverol Y.,Center for Genetic Engineering and Biotechnology | Perez-Riverol Y.,European Bioinformatics Institute | Hermjakob H.,European Bioinformatics Institute | Kohlbacher O.,University of Tubingen | And 18 more authors.
Journal of Proteomics | Year: 2013

The workshop "Bioinformatics for Biotechnology Applications (HavanaBioinfo 2012)", held December 8-11, 2012 in Havana, aimed at exploring new bioinformatics tools and approaches for large-scale proteomics, genomics and chemoinformatics. Major conclusions of the workshop include the following: (i) development of new applications and bioinformatics tools for proteomic repository analysis is crucial; current proteomic repositories contain enough data (spectra/identifications) that can be used to increase the annotations in protein databases and to generate new tools for protein identification; (ii) spectral libraries, de novo sequencing and database search tools should be combined to increase the number of protein identifications; (iii) protein probabilities and FDR are not yet sufficiently mature; (iv) computational proteomics software needs to become more intuitive; and at the same time appropriate education and training should be provided to help in the efficient exchange of knowledge between mass spectrometrists and experimental biologists and bioinformaticians in order to increase their bioinformatics background, especially statistics knowledge. © 2013 Elsevier B.V.

Zhang J.,Bioinformatics Solutions Inc.
Molecular & cellular proteomics : MCP | Year: 2012

Many software tools have been developed for the automated identification of peptides from tandem mass spectra. The accuracy and sensitivity of the identification software via database search are critical for successful proteomics experiments. A new database search tool, PEAKS DB, has been developed by incorporating the de novo sequencing results into the database search. PEAKS DB achieves significantly improved accuracy and sensitivity over two other commonly used software packages. Additionally, a new result validation method, decoy fusion, has been introduced to solve the issue of overconfidence that exists in the conventional target decoy method for certain types of peptide identification software.

Zhang Z.,Bioinformatics Solutions Inc. | Lin H.,University of Waterloo | Ma B.,University of Waterloo
Nucleic Acids Research | Year: 2010

High-throughput next-generation sequencing technologies pose increasing demands on the efficiency, accuracy and usability of data analysis software. In this article, we present ZOOM Lite, a software for efficient reads mapping and result visualization. With a kernel capable of mapping tens of millions of Illumina or AB SOLiD sequencing reads efficiently and accurately, and an intuitive graphical user interface, ZOOM Lite integrates reads mapping and result visualization into a easy to use pipeline on desktop PC. The software handles both single-end and paired-end reads, and can output both the unique mapping result or the top N mapping results for each read. Additionally, the software takes a variety of input file formats and outputs to several commonly used result formats. The software is freely available at http://bioinfor.com/zoom/lite/. © The Author(s) 2010. Published by Oxford University Press.

Bioinformatics Solutions Inc. | Date: 2011-06-28

Bioinformatics Software for analyzing data acquired from mass spectrometry instruments for the purpose of identifying protein glycosylation.

Bioinformatics Solutions Incorporated | Date: 2008-09-16

Computer software for protein mass spectrometry data analysis.

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