Codon-usage bias has been observed in almost all genomes and is thought to result from selection for efficient and accurate translation of highly expressed genes. Codon usage is also implicated in the control of transcription, splicing and RNA structure. Many genes exhibit little codon-usage bias, which is thought to reflect a lack of selection for messenger RNA translation. Alternatively, howe...

SUMMARY We describe miTRATA, the first web-based tool for microRNA Truncation and Tailing Analysis--the analysis of 3' modifications of microRNAs including the loss or gain of nucleotides relative to the canonical sequence. miTRATA is implemented in Python (version 3) and employs parallel processing modules to enhance its scalability when analyzing multiple small RNA (sRNA) sequencing datasets....

in order to study physiological characteristics of rainfed bread wheat genotypes, an experiment was conducted with 20 genotypes in a randomized complete block design with 4 replications under rainfed and supplementary irrigation conditions. this experiment was carried out at the dryland agricultural research institute (dari) in maragheh during 2007-2008. to determine growth indices, sampling wa...

SUMMARY Peptide identification algorithm is a major bottleneck for mass spectrometry based chemical cross-linking experiments. Our lab recently developed an intensity-incorporated peptide identification algorithm, and here we implemented this scheme for cross-linked peptide discovery. Our program, SQID-XLink, searches all regular, dead-end, intra and inter cross-linked peptides simultaneously, ...

UNLABELLED Finding related conformations in the Protein Data Bank is essential in many areas of bioscience. To assist this task, we designed a dihedral angle database for searching protein segment homologs. The search engine relies on encoding of the protein coordinates into text characters representing amino acid sequence, φ and ψ dihedral angles. The search engine is advantageous owing to its...

UNLABELLED EpiToolKit is a virtual workbench for immunological questions with a focus on vaccine design. It offers an array of immunoinformatics tools covering MHC genotyping, epitope and neo-epitope prediction, epitope selection for vaccine design, and epitope assembly. In its recently re-implemented version 2.0, EpiToolKit provides a range of new functionality and for the first time allows co...

The seemingly unrelated Poisson (SUP) model (King (1989a), see also Aptech (1994)) is a model for bior multi-variate counted outcomes. Correlation between equations is introduced through a convolution structure with a common additive factor. Previous economic applications include the joint analysis of voluntary and involuntary labour mobility (Jung and Winkelmann, 1993) and the number of recrea...

SUMMARY We have developed a novel Bayesian method, PurBayes, to estimate tumor purity and detect intratumor heterogeneity based on next-generation sequencing data of paired tumor-normal tissue samples, which uses finite mixture modeling methods. We demonstrate our approach using simulated data and discuss its performance under varying conditions. AVAILABILITY PurBayes is implemented as an R p...