Interpolative multidimensional scaling techniques for the identification of clusters in very large sequence sets.

Background: Modern pyrosequencing techniques make it possible to study complex bacterial populations, such as 16S rRNA, directly from environmental or clinical samples without the need for laboratory purification. Alignment of sequences across the resultant large data sets (100,000+ sequences) is of particular interest for the purpose of identifying potential gene clusters and families, but such analysis represents a daunting computational task. The aim of this work is the development of an efficient pipeline for the clustering of large sequence read sets.

Hybrid cloud and cluster computing paradigms for life science applications.

Background: Clouds and MapReduce have shown themselves to be a broadly useful approach to scientific computing especially for parallel data intensive applications. However they have limited applicability to some areas such as data mining because MapReduce has poor performance on problems with an iterative structure present in the linear algebra that underlies much data analysis. Such problems can be run efficiently on clusters using MPI leading to a hybrid cloud and cluster environment.

dPattern: transcription factor binding site (TFBS) discovery in human genome using a discriminative pattern analysis.

Motivation: Transcription factor binding sites (TFBSs) are typically short in length, thus search with a profile model from known TFBSs produces many false positives. When combined with additional information, gene expression data in this article, sensitivity and specificity of TFBS search can be improved significantly.

Results: By modifying our previous REFINEMENT approach, we developed dPattern that searches for occurrences of TFBSs in the promotor regions of up/down regulated or random genes.

Crystallization and preliminary X-ray crystallographic analysis of acetohydroxy acid isomeroreductase from Pseudomonas aeruginosa.

Acetohydroxy acid isomeroreductase (AHIR) is involved in the biosynthetic pathway of branched-chain amino acids in microorganisms and plants. AHIR from Pseudomonas aeruginosa has been overexpressed in Escherichia coli and crystallized at 297 K using potassium/sodium tartrate as a precipitant. X-ray diffraction data have been collected to 2.