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Available from: Gajendra Pal Singh Raghava, Aug 14, 2015
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    • "The front page of BlockLogo with an example of input for the visualization of region 220–229 of MSA of influenza A HA. Numbering is relative to the MSA alignment position and the input in this example is in the FASTA format. 2008a, 2008b; Zhang et al. 2011). When the HLA binding prediction option is selected, netMHC is used to predict HLA class I binders if the selected block is of length 8–11, and for HLA class II binders if the selected block is of length 13–25. "
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    ABSTRACT: BlockLogo is a web-server application for visualization of protein and nucleotide fragments, continuous protein sequence motifs, and discontinuous sequence motifs using calculation of block entropy from multiple sequence alignments. The user input consists of a multiple sequence alignment, selection of motif positions, type of sequence, and output format definition. The output has BlockLogo along with the sequence logo, and a table of motif frequencies. We deployed BlockLogo as an online application and have demonstrated its utility through examples that show visualization of T-cell epitopes and B-cell epitopes (both continuous and discontinuous). Our additional example shows a visualization and analysis of structural motifs that determine specificity of peptide binding to HLA-DR molecules. The BlockLogo server also employs selected experimentally validated prediction algorithms to enable on-the-fly prediction of MHC binding affinity to 15 common HLA class I and class II alleles as well as visual analysis of discontinuous epitopes from multiple sequence alignments. It enables the visualization and analysis of structural and functional motifs that are usually described as regular expressions. It provides a compact view of discontinuous motifs composed of distant positions within biological sequences. BlockLogo is available at: http://research4.dfci.harvard.edu/cvc/blocklogo/ and http://met-hilab.bu.edu/blocklogo/
    Journal of immunological methods 08/2013; 400-401. DOI:10.1016/j.jim.2013.08.014 · 2.01 Impact Factor
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    ABSTRACT: The immune system is characterized by high combinatorial complexity that necessitates the use of specialized computational tools for analysis of immunological data. Machine learning (ML) algorithms are used in combination with classical experimentation for the selection of vaccine targets and in computational simulations that reduce the number of necessary experiments. The development of ML algorithms requires standardized data sets, consistent measurement methods, and uniform scales. To bridge the gap between the immunology community and the ML community, we designed a repository for machine learning in immunology named Dana-Farber Repository for Machine Learning in Immunology (DFRMLI). This repository provides standardized data sets of HLA-binding peptides with all binding affinities mapped onto a common scale. It also provides a list of experimentally validated naturally processed T cell epitopes derived from tumor or virus antigens. The DFRMLI data were preprocessed and ensure consistency, comparability, detailed descriptions, and statistically meaningful sample sizes for peptides that bind to various HLA molecules. The repository is accessible at http://bio.dfci.harvard.edu/DFRMLI/.
    Journal of immunological methods 07/2011; 374(1-2):18-25. DOI:10.1016/j.jim.2011.07.007 · 2.01 Impact Factor
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    ABSTRACT: Prediction methods as well as experimental methods for T-cell epitope discovery have developed significantly in recent years. High-throughput experimental methods have made it possible to perform full-length protein scans for epitopes restricted to a limited number of MHC alleles. The high costs and limitations regarding the number of proteins and MHC alleles that are feasibly handled by such experimental methods have made in silico prediction models of high interest. MHC binding prediction methods are today of a very high quality and can predict MHC binding peptides with high accuracy. This is possible for a large range of MHC alleles and relevant length of binding peptides. The predictions can easily be performed for complete proteomes of any size. Prediction methods are still, however, dependent on good experimental methods for validation, and should merely be used as a guide for rational epitope discovery. We expect prediction methods as well as experimental validation methods to continue to develop and that we will soon see clinical trials of products whose development has been guided by prediction methods.
    Expert Review of Vaccines 01/2012; 11(1):43-54. DOI:10.1586/erv.11.160 · 4.22 Impact Factor
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