Current Bioinformatics - Volume 5, Issue 1, 2010

Copy number alterations (CNA) in genomic DNA are linked to a variety of human diseases. Although many methods have been developed to analyze data from a single subject, disease-critical genes are more likely to be found in regions that are common or recurrent among diseased subjects. Unfortunately, finding recurrent CNA regions remains a challenge. We review existing methods for the identification of recurre Read More

Single nucleotide polymorphism (SNP) is the predominant form of human genetic variation, and is widely used in disease association studies. Haplotype, i.e. a sequence of SNPs on a chromosome, can provide more information than single SNPs. Haplotype-based analysis is more powerful in complex disease association studies than SNP-based methods. However, it is much difficult to determine haplotypes using only biologi Read More

The aim of many microarray experiments is to build discriminatory diagnosis and prognosis models. A large number of supervised methods have been proposed in literature for microarray-based classification. Model comparison, which is based on the classification error estimation, is a critical issue. Previous studies have shown that error estimation is unreliable in high-dimensional small-sample settings. This leads naturally to q Read More

Genetic data is often used to infer evolutionary relationships among a collection of viruses, bacteria, animal or plant species, or other operational taxonomic units (OTU). A phylogenetic tree depicts such relationships and provides a visual representation of the estimated branching order of the OTUs. Tree estimation is unique for several reasons, including the types of data used to represent each OTU; the use of probabilistic nuc Read More

Classification in bioinformatics often suffers from small samples in conjunction with large numbers of features, which makes error estimation problematic. When a sample is small, there is insufficient data to split the sample and the same data are used for both classifier design and error estimation. Error estimation can suffer from high variance, bias, or both. The problem of choosing a suitable error estimator is exacerba Read More

In recent years, increasingly sophisticated computational and bioinformatics tools have evolved for the analyses of protein structure, function, ligand interactions, modeling and energetics. This includes the development of algorithms to recursively evaluate side-chain rotamer permutations, identify regions in a 3D structure that meet some set of search parameters, calculate and minimize energy values, and provide high-res Read More

MicroRNAs (miRNA) are small non-coding RNA molecules involved in the posttranscriptional regulation of gene expression. miRNAs bind specifically to the 3' untranslated region of messenger RNA (mRNA) molecules and induce translational repression or mRNA degradation. Potential miRNA targets can be predicted by various computational algorithms that take several parameters into consideration and calculate probability Read More