Plotting SRA database growth

The Sequence Read Archive is NCBI’s database for high throughput sequencing data and the largest public repository for such data. The data on the growth of the database is available here

The BORDER family of negative transcription elongation factors regulates flowering time in Arabidopsis

- BDR proteins repress expression of the floral repressor, FLC - BDR proteins physically interact with the autonomous pathway protein FPA - BDR-repressed genes have high levels of Pol II occupancy, despite low mRNA levels - Gene repression by BDR may involve the inhibition of transcription elongation

Widespread premature transcription termination of Arabidopsis thaliana NLR genes by the spen protein FPA

Genes involved in disease resistance are some of the fastest evolving and most diverse components of genomes. Large numbers of nucleotide-binding, leucine-rich repeat (NLR) genes are found in plant genomes and are required for disease resistance. …

The 7SK/P-TEFb snRNP controls ultraviolet radiation-induced transcriptional reprogramming

- The 7SK snRNA is dispensable for cell proliferation under standard growth conditions - After UV exposure, 7SK/P-TEFb is needed for proper stress response and cell survival - P-TEFb extracted from 7SK/P-TEFb triggers UV-induced general RNAPII pause release - P-TEFb from 7SK/P-TEFb supports activation of important UV-responsive genes

Blastn output format 6

See also: Blast documentation Blast on Metagenomics Wiki blastn -help and check -outfmt formatting option Prepare the database Only needed if reference sequences are going to be used frequently

Bioinformatics and Biostatistics

Tools for the analysis and integration of high throughput data

Chromatin and Transcription

Transcription by RNA polymerase II in the context of chromatin

BORDER proteins protect expression of neighboring genes by promoting 3' Pol II pausing in plants

Ensuring that one gene's transcription does not inappropriately affect the expression of its neighbors is a fundamental challenge to gene regulation in a genomic context. In plants, which lack homologs of animal insulator proteins, the mechanisms …

Core bioconductor packages for NGS data analysis

CCA: An R Package to Extend Canonical Correlation Analysis

Canonical correlations analysis (CCA) is an exploratory statistical method to highlight correlations between two data sets acquired on the same experimental units. The cancor() function in R (R Development Core Team 2007) performs the core of …