SEWAL: an open-source platform for next-generation sequence analysis and visualization

Next-generation DNA sequencing platforms provide exciting new possibilities for in vitro genetic analysis of functional nucleic acids. However, the size of the resulting data sets presents computational and analytical challenges. We present an open-source software package that employs a locality-sensitive hashing algorithm to enumerate all unique sequences in an entire Illumina sequencing run (∼10⁸ sequences). The algorithm results in quasilinear time processing of entire Illumina lanes (∼10⁷ sequences) on a desktop computer in minutes. To facilitate visual analysis of sequencing data, the software produces three-dimensional scatter plots similar in concept to Sewall Wright and John Maynard Smith’s adaptive or fitness landscape. The software also contains functions that are particularly useful for doped selections such as mutation frequency analysis, information content calculation, multivariate statistical functions (including principal component analysis), sequence distance metrics, sequence searches and sequence comparisons across multiple Illumina data sets. Source code, executable files and links to sample data sets are available at http://www.sourceforge.net/projects/sewal.     

xGDB: open-source computational infrastructure for the integrated evaluation and analysis of genome features

The eXtensible Genome Data Broker (xGDB) provides a software infrastructure consisting of integrated tools for the storage, display, and analysis of genome features in their genomic context. Common features include gene structure annotations, spliced alignments, mapping of repetitive sequence, and microarray probes, but the software supports inclusion of any property that can be associated with a genomic location. The xGDB distribution and user support utilities are available online at the xGDB project website, http://xgdb.sourceforge.net/.     

Contractile properties of the functionally divided python heart: two sides of the same matter

The heart of Python regius is functionally divided so that systemic blood pressure is much higher than pulmonary pressure (6.6+/-1.0 and 0.7+/-0.1 kPa, respectively). The present study shows that force production of cardiac strips from the cavum arteriosum and cavum pulmonale exhibits similar force production when stimulated in vitro. The high systemic blood pressure is caused, therefore, by a thicker ventricular wall surrounding the cavum arteriosum rather than differences in the intrinsic properties of the cardiac tissues. Similarly, there were no differences between the contractile properties of right and left atria. Force production was similar in atria and ventricle but the atria contracted and relaxed much faster than the ventricle. Graded hypoxia markedly reduced twitch force of all four cardiac tissues, and this was most pronounced when PO(2) was below 40 kPa. In contrast, the four cardiac tissues were insensitive to acidosis during normoxia although acidosis increased the sensitivity to hypoxia. Adrenergic stimulation increased twitch force of all cardiac tissues, while cholinergic stimulation only affected the atria and reduced twitch force markedly. In spite of the different oxygen availability of the two sides of the heart, the biochemical and functional properties are alike and the differences may instead be overcome by the coronary blood supply.     

Mechanical properties of calcified exoskeleton from the neotropical millipede, Nyssodesmus python

The calcified exoskeleton of millipedes plays a crucial role in resisting large forces developed during burrowing locomotion. I measured morphological and mechanical properties of cuticle from the neotropical forest floor millipede, Nyssodesmus python (Diplopoda: Polydesmidae), which ranges in body mass from 2 to 7 g. Scaling of thickness of the cuticle with respect to body mass followed predictions of geometric similarity. Both fracture strength and Young's modulus increased with body mass in females but not in males. In spite of their smaller size, male millipedes were still stronger, on average, than female millipedes. Mean fracture strength of millipede cuticle was 124 MPa, and Young's modulus was 17 GPa. Both of these values exceed measurements from typical insect cuticle, suggesting that calcium salts may play a role in stiffening and strengthening the millipede exoskeleton. Because of the high density of calcified millipede cuticle (1660 kg/m³), stiffness and strength relative to body weight remain comparable to values for other insect cuticles. These results corroborate a previous hypothesis that absolute not specific strength and stiffness have been selective factors in the evolution of millipede cuticle, and that bulkiness of the exoskeleton has been minimized through the deposition of calcium salts.     

The analysis and application of a recombinant monooxygenase library as a biocatalyst for the Baeyer-Villiger reaction

Because of their selectivity and catalytic efficiency, BVMOs are highly valuable biocatalysts for the chemoenzymatic synthesis of a broad range of useful compounds. In this study, we investigated the microbial Baeyer-Villiger oxidation and sulfoxidation of thioanisole and bicyclo[3.2.0]hept-2-en-6-one using whole Escherichia coli cells that recombined with each of the Baeyer-Villiger monooxygenases originated from Pseudomonas aeruginosa PAO1 and two from Streptomyces coelicolor A3(2). The three BVMOs were identified in the microbial genome database by a recently described protein sequence motif; e.g., BVMO motif (FXGXXXHXXXW). The reaction products were identified as (R)-/(S)sulfoxide and 2-oxabicyclo/3-oxabicyclo[3.3.0]oct-6-en-2-one by GC-MS analysis. Consequently, this study demonstrated that the three enzymes can indeed catalyze the Baeyer-Villiger reaction as a biocatalyst, and effective annotation tools can be efficiently exploited as a source of novel BVMOs.     

GenomeDiagram: a python package for the visualization of large-scale genomic data

SUMMARY: We present GenomeDiagram, a flexible, open-source Python module for the visualization of large-scale genomic, comparative genomic and other data with reference to a single chromosome or other biological sequence. GenomeDiagram may be used to generate publication-quality vector graphics, rastered images and in-line streamed graphics for webpages. The package integrates with datatypes from the BioPython project, and is available for Windows, Linux and Mac OS X systems. AVAILABILITY: GenomeDiagram is freely available as source code (under GNU Public License) at http://bioinf.scri.ac.uk/lp/programs.html, and requires Python 2.3 or higher, and recent versions of the ReportLab and BioPython packages. SUPPLEMENTARY INFORMATION: A user manual, example code and images are available at http://bioinf.scri.ac.uk/lp/programs.html.     

Phylogeographic analysis of the green python,Morelia viridis,reveals cryptic diversity

Green pythons, which are regionally variable in colour patterns, are found throughout the lowland rainforest of New Guinea and adjacent far northeastern Australia. The species is popular in commercial trade and management of this trade and its impacts on natural populations could be assisted by molecular identification tools. We used mitochondrial nucleotide sequences and a limited allozyme data to test whether significantly differentiated populations occur within the species range. Phylogenetic analysis of mtDNA sequences revealed hierarchal phylogeographic structure both within New Guinea and between New Guinea and Australia. Strongly supported reciprocally monophyletic mitochondrial lineages, northern and southern, were found either side of the central mountain range that runs nearly the length of New Guinea. Limited allozyme data suggest that population differentiation is reflected in the nuclear as well as the mitochondrial genome. A previous morphological analysis did not find any phenotypic concordance with the pattern of differentiation observed in the molecular data. The southern mitochondrial lineage includes all of the Australian haplotypes, which form a single lineage, nested among the southern New Guinean haplotypes.     

GenABEL: an R library for genome-wide association analysis

Here we describe an R library for genome-wide association (GWA) analysis. It implements effective storage and handling of GWA data, fast procedures for genetic data quality control, testing of association of single nucleotide polymorphisms with binary or quantitative traits, visualization of results and also provides easy interfaces to standard statistical and graphical procedures implemented in base R and special R libraries for genetic analysis. We evaluated GenABEL using one simulated and two real data sets. We conclude that GenABEL enables the analysis of GWA data on desktop computers. Availability: http://cran.r-project.org.     

BiNChE: A web tool and library for chemical enrichment analysis based on the ChEBI ontology

Background

Ontology-based enrichment analysis aids in the interpretation and understanding of large-scale biological data. Ontologies are hierarchies of biologically relevant groupings. Using ontology annotations, which link ontology classes to biological entities, enrichment analysis methods assess whether there is a significant over or under representation of entities for ontology classes. While many tools exist that run enrichment analysis for protein sets annotated with the Gene Ontology, there are only a few that can be used for small molecules enrichment analysis.

Results

We describe BiNChE, an enrichment analysis tool for small molecules based on the ChEBI Ontology. BiNChE displays an interactive graph that can be exported as a high-resolution image or in network formats. The tool provides plain, weighted and fragment analysis based on either the ChEBI Role Ontology or the ChEBI Structural Ontology.

Conclusions

BiNChE aids in the exploration of large sets of small molecules produced within Metabolomics or other Systems Biology research contexts. The open-source tool provides easy and highly interactive web access to enrichment analysis with the ChEBI ontology tool and is additionally available as a standalone library.

Electronic supplementary material

The online version of this article (doi:10.1186/s12859-015-0486-3) contains supplementary material, which is available to authorized users.     

Application of characteristic reaction paths: Rate-limiting capability of phosphofructokinase in yeast fermentation

The intracellular rate-limiting capability of phosphofructokinase in baker's yeast (Saccharomyces cerevisiae) fermentation is investigated using the reaction path analysis discussed by Liao and Lightfoot in a previous article. It is found that the yeast cells under our experimental conditions indeed exhibit the characteristic behavior, and the characteristic reaction path on the G6P-ATP phase plot is determined for cells fed with different sugars, cells of different strains, and cells in the transition period following rehydration. Results suggest that phosphofructokinase does not limit the CO(2) production rate of the cells under investigation. However, it is not present in a great excess either: ca. 80% of phosphofructokinase activity is utilized by the glycolytic pathway of the cell under investigation.     

Analysis for free: comparing programs for sequence analysis

Programs to import, manage and align sequences and to analyse the properties of DNA, RNA and proteins are essential for every biological laboratory. This review describes two different freeware (BioEdit and pDRAW for MS Windows) and a commercial program (Sequencher for MS Windows and Apple MacOS). Bioedit and Sequencher offer functions such as sequence alignment and editing plus reading of sequence trace files. pDRAW is a very comfortable visualisation tool with a variety of analysis functions. While Sequencher impresses with a very user-friendly interface and easy-to-use tools, BioEdit offers the largest and most customisable variety of tools. The strength of pDRAW is drawing and analysis of single sequences for priming and restriction sites and virtual cloning. It has a database function for user-specific oligonucleotides and restriction enzymes.