Kevin Karplus' research group develops tools and techniques for genome assembly from next-generation sequence data, signal processing and machine learning for nanopores.
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PREDICT-2ND: a tool for generalized protein local structure prediction.
Published in Bioinformatics
Complete genome sequence of Pyrobaculum oguniense.
Published in Standards in Genomic Sciences
Pyrobaculum oguniense TE7 is an aerobic hyperthermophilic crenarchaeon isolated from a hot spring in Japan. Here we describe its main chromosome of 2,436,033 bp, with three large-scale inversions and an extra-chromosomal element of 16,887 bp. We have annotated 2,800 protein-coding genes and 145 RNA genes in this genome, including nine H/ACA-like sm...
SAM-T04: what is new in protein-structure prediction for CASP6.
Published in Proteins Structure Function and Bioinformatics
The SAM-T04 method for predicting protein structures uses a single protocol across the entire range of targets, from comparative modeling to new folds. This protocol is similar to the SAM-T02 protocol used in CASP5, but has improvements in the iterative search for similar sequences in finding and aligning templates, in creating fragment libraries, ...
