SpliceGrapher: detecting patterns of alternative splicing from RNA-Seq data in the context of gene models and EST data

We propose a method for predicting splice graphs that enhances curated gene models using evidence from RNA-Seq and EST alignments. Results obtained using RNA-Seq experiments in Arabidopsis thaliana show that predictions made by our SpliceGrapher method are more consistent with current gene models than predictions made by TAU and Cufflinks. Furthermore, analysis of plant and human data indicates that the machine learning approach used by SpliceGrapher is useful for discriminating between real and spurious splice sites, and can improve the reliability of detection of alternative splicing. SpliceGrapher is available for download at .     

Kinesins in the Arabidopsis genome: A comparative analysis among eukaryotes

Background  

Receptor protein tyrosine phosphatase rho (RPTPρ, gene symbol PTPRT) is a member of the type IIB RPTP family. These transmembrane molecules have been linked to signal transduction, cell adhesion and neurite extension. The extracellular segment contains MAM, Ig-like and fibronectin type III domains, and the intracellular segment contains two phosphatase domains. The human RPTPρ gene is located on chromosome 20q12-13.1, and the mouse gene is located on a syntenic region of chromosome 2. RPTPρ expression is restricted to the central nervous system.     

The attitudes of riparian communities to the presence of water hyacinth in the Wouri River Basin,Douala, Cameroon

Since publication of the first record of Eichhornia crassipes in Cameroon in 1997, the weed has become highly invasive in the Wouri River Basin. Between June and September 2014, a socio-economic survey using participatory and qualitative methods was undertaken in the riparian villages of the Wouri River Basin to assess the perception of respondents to the presence of water hyacinth. The survey revealed that water hyacinth was a significant threat to activities along the river, which included fishing, sand extraction and river transportation. The presence of water hyacinth mats reduced catch rates of several common fish species, river transportation by 75%, and significantly reduced the income for sand extraction. Cameroon employs manual clearing of water hyacinth; however, respondents indicated they would consider other control methods, provided they do not have any negative impacts.