Gene expression rate comparison for multiple high-throughput datasets.

Microarray provides genome-wide transcript profiles, whereas RNA-seq is an alternative approach applied for transcript discovery and genome annotation. Both high-throughput techniques show quantitative measurement of gene expression. To explore differential gene expression rates and understand biological functions, the authors designed a system which utilises annotations from Kyoto Encyclopedia of Genes and Genomes (KEGG) biological pathways and Gene Ontology (GO) associations for integrating multiple RNA-seq or microarray datasets. The developed system is initiated by either estimating gene expression levels from mapping next generation sequencing short reads onto reference genomes or performing intensity analysis from microarray raw images. Normalisation procedures on expression levels are evaluated and compared through different approaches including Reads Per Kilobase per Million mapped reads (RPKM) and housekeeping gene selection. Such gene expression levels are shown in different colour shades and graphically displayed in designed temporal pathways. To enhance importance of functional relationships of clustered genes, representative GO terms associated with differentially expressed gene cluster are visually illustrated in a tag cloud representation.

BiMFG: bioinformatics tools for marine and freshwater species.

Biomolecule sequences and structures of land, air and water species are determined rapidly and the data entries are unevenly distributed for different organisms. It frequently leads to the BLAST results of homologous search containing undesirable entries from organisms living in different environments. To reduce irrelevant searching results, a separate database for comparative genomics is urgently required. A comprehensive bioinformatics tool set and an integrated database, named Bioinformatics tools for Marine and Freshwater Genomics (BiMFG), are constructed for comparative analyses among model species and underwater species. Novel matching techniques based on conserved motifs and/or secondary structure elements are designed for efficiently and effectively retrieving and aligning remote sequences through cross-species comparisons. It is especially helpful when sequences under analysis possess low similarities and unresolved structural information. In addition, the system provides core techniques of multiple sequence alignment, multiple second structure profile alignment and iteratively refined multiple structural alignments for biodiversity analysis and verification in marine and freshwater biology. The BiMFG web server is freely available for use at http://bimfg.cs.ntou.edu.tw/.