Determining the number of contributors to a genetic sample is usually a necessary step towards accurately using the information experimentally. This determination is often made using naive approaches. An error in this determination may cast doubt on the accuracy of the final conclusion. Nowhere is the importance of this issue more obvious than in the forensic testing of human DNA. In forensic testing, a misinterpretation of the number of contributors to a genetic mixture may make the difference between justice and injustice. Computational methods may take into account not only naive features (such as the number and magnitude of genetic markers), but also the frequency of occurrence of these markers in the general population. Use of this additional information allows the determination of li…

A B-cell epitope is a part of an antigen that is recognized by a specific antibody or B-cell receptor. Detecting the immunogenic region of the antigen is useful in numerous immunodetection and immunotherapeutics applications. The aim of this paper is to find relevant properties to discriminate the location of potential epitopes from the rest of the protein surface. The most relevant properties, identified using two evaluation approaches, are the geometric properties, followed by the conservation score and some chemical properties, such as the proportion of glycine. The selected properties are used in a patch based epitope localization method including a Single Layer Perceptron for regression. The output of this Single Layer Perceptron is used to construct a probability map on the antigen s…

A large numberof unclassified sequences is still found in public databases, which suggests that there is still need for new investigations in the area. In this contribution, we present a methodology based on Artificial Neural Networks for protein functional classification. A new protein coding scheme, called here Extended-Sequence Coding by Sliding Windows, is presented with the goal of overcoming some of the difficulties of the well method Sequence Coding by Sliding Window. The new protein coding scheme uses more than one sliding window length with a weight factor that is proportional to the window length, avoiding the ambiguity problem without ignoring the identity of small subsequences Accuracy for Sequence Coding by Sliding Windows ranged from 60.1% to 77.7% for the first bacterium pro…

A reliable and precise identification of the type of tumors is crucial to the effective treatment of cancer. With the rapid development of microarray technologies, tumor clustering based on gene expression data is becoming a powerful approach to cancer class discovery. In this paper, we apply the penalized matrix decomposition (PMD) to gene expression data to extract metasamples for clustering. The extracted metasamples capture the inherent structures of samples belong to the same class. At the same time, the PMD factors of a sample over the metasamples can be used as its class indicator in return. Compared with the conventional methods such as hierarchical clustering (HC), self-organizing maps (SOM), affinity propagation (AP) and non-negative matrix factorization (NMF), the proposed metho…

We present the results of a competitive analysis of our method against other approaches. The analysis was conducted on data from plasma/ethylenediaminetetraacetic acid (EDTA) of “control” and Alzheimer patients collected from three different hospitals. The results point to a significant performance advantage of our method with respect to the competing ones tested. (Source: IEEE/ACM Transactions on Computational Biology and Bioinformatics)

Conclusions:
The Proteogenomic Mapping Tool provides a standalone application for mapping peptides back to their source genome on a number of operating system platforms with standard desktop computer hardware and executes very rapidly for a variety of datasets. Allowing the selection of different genetic codes for different organisms allows researchers to easily customize the tool to their own research interests and is recommended for anyone working to structurally annotate genomes using MS derived proteomics data. (Source: BMC Bioinformatics – Latest articles)

Conclusions:
Comparing state-of-the-art software, SiLiX presents the best up-to-date capabilities to face the problem of clustering large collections of sequences. SiLiX is freely available at http://lbbe.univ-lyon1.fr/silix. (Source: BMC Bioinformatics – Latest articles)

Conclusions:
The MI-GWAS platform provides a valuable tool for the analysis of association of a phenotype or condition with maternal and inherited genotypes using genome-wide data from case-parent triads. The source code for this platform is freely available at http://www.sph.uth.tmc.edu/sbrr/mi-gwas.htm. (Source: BMC Bioinformatics – Latest articles)

Conclusion: MiR‐1 regulates the expression of several host genes to enhance HBV replication and reverse cancer cell phenotype, which is apparently beneficial for HBV replication. Our findings provide a novel perspective on the role of miRNAs in host‐virus interactions in HBV infection. (HEPATOLOGY 2011;) (Source: Hepatology)

Authors: Uehara H, Iwasaki Y, Wada C, Ikemura T, Abe T
Although remarkable progress in metagenomic sequencing of various environmental samples has been made, large numbers of fragment sequences have been registered in the international DNA databanks, primarily without information on gene function and phylotype, and thus with limited usefulness. Industrial useful biological activity is often carried out by a set of genes, such as those constituting an operon. In this connection, metagenomic approaches have a weakness because sets of the genes are usually split up, since the sequences obtained by metagenome analyses are fragmented into 1-kb or much shorter segments. Therefore, even when a set of genes responsible for an industrially useful function is found in one metagenome library, it …