RNA-clique: a method for computing genetic distances from RNA-seq data.

Background: Although RNA-seq data are traditionally used for quantifying gene expression levels, the same data could be useful in an integrated approach to compute genetic distances as well. Challenges to using mRNA sequences for computing genetic distances include the relatively high conservation of coding sequences and the presence of paralogous and, in some species, homeologous genes.

Results: We developed a new computational method, RNA-clique, for calculating genetic distances using assembled RNA-seq data and assessed the efficacy of the method using biological and simulated data.

Rapid and Reusable Text Visualization and Exploration Development with DELVE.

We present DELVE (Document ExpLoration and Visualization Engine), a framework for developing interactive visualizations as modular Web-applications to assist researchers with exploratory literature search. The goal for web-applications driven by DELVE is to better satisfy the information needs of researchers and to help explore and understand the state of research in scientific liter ature by providing immersive visualizations that both contain facets and are driven by facets derived from the literature. We base our framework on principles from user-centered design and human-computer interaction (HCI).

Swainsonine Biosynthesis Genes in Diverse Symbiotic and Pathogenic Fungi.

Swainsonine-a cytotoxic fungal alkaloid and a potential cancer therapy drug-is produced by the insect pathogen and plant symbiont , the clover pathogen , locoweed symbionts belonging to sect. , and a recently discovered morning glory symbiont belonging to order Chaetothyriales. Genome sequence analyses revealed that these fungi share orthologous gene clusters, designated "," which included a multifunctional gene comprising predicted adenylylation and acyltransferase domains with their associated thiolation domains, a β-ketoacyl synthase domain, and two reductase domains.

Proceedings of the 15th Annual UT-KBRIN Bioinformatics Summit 2016 : Cadiz, KY, USA. 8-10 April 2016.

I1 Proceedings of the Fifteenth Annual UT- KBRIN Bioinformatics Summit 2016 Eric C. Rouchka, Julia H. Chariker, Benjamin J.

Plant-symbiotic fungi as chemical engineers: multi-genome analysis of the clavicipitaceae reveals dynamics of alkaloid loci.

The fungal family Clavicipitaceae includes plant symbionts and parasites that produce several psychoactive and bioprotective alkaloids. The family includes grass symbionts in the epichloae clade (Epichloë and Neotyphodium species), which are extraordinarily diverse both in their host interactions and in their alkaloid profiles. Epichloae produce alkaloids of four distinct classes, all of which deter insects, and some-including the infamous ergot alkaloids-have potent effects on mammals.

A linear-time algorithm for finding a maximum-length ORF in a splice graph.

We present a linear-time, deterministic algorithm for finding a longest Open Reading Frame (ORF) in an alternatively spliced gene represented by a splice graph. Finding protein-encoding regions is a fundamental problem in genomic and transcriptomic analysis, and in some circumstances long ORFs can provide good predictions of such regions. Splice graphs are a common way of compactly representing what may be exponentially many alternative splicings of a sequence.

Statistical phylogenetic tree analysis using differences of means.

We propose a statistical method to test whether two phylogenetic trees with given alignments are significantly incongruent. Our method compares the two distributions of phylogenetic trees given by two input alignments, instead of comparing point estimations of trees. This statistical approach can be applied to gene tree analysis for example, detecting unusual events in genome evolution such as horizontal gene transfer and reshuffling.

Analysis of chameleon sequences and their implications in biological processes.

Chameleon sequences have been implicated in amyloid related diseases. Here we report an analysis of two types of chameleon sequences, chameleon-HS (Helix vs. Strand) and chameleon-HE (Helix vs.