Summary: ChronQC is a quality control (QC) tracking system for clinical implementation of next-generation sequencing (NGS). ChronQC generates time series plots for various QC metrics to allow comparison of current runs to historical runs. ChronQC has multiple features for tracking QC data including Westgard rules for clinical validity, laboratory-defined thresholds and historical observations within a specified time period. Users can record their notes and corrective actions directly onto the plots for long-term recordkeeping. ChronQC facilitates regular monitoring of clinical NGS to enable adherence to high quality clinical standards. Availability and implementation: ChronQC is freely available on GitHub (https://github.com/nilesh-tawari/ChronQC), Docker (https://hub.docker.com/r/nileshtawari/chronqc/) and the Python Package Index. ChronQC is implemented in Python and runs on all common operating systems (Windows, Linux and Mac OS X). Contact: [email protected] or [email protected]. Supplementary information: Supplementary data are available at Bioinformatics online.

Social networks readily transmit information, albeit with less than perfect fidelity. We present a large-scale measurement of this imperfect information copying mechanism by examining the dissemination and evolution of thousands of memes, collectively replicated hundreds of millions of times in the online social network Facebook. The information undergoes an evolutionary process that exhibits several regularities. A meme's mutation rate characterizes the population distribution of its variants, in accordance with the Yule process. Variants further apart in the diffusion cascade have greater edit distance, as would be expected in an iterative, imperfect replication process. Some text sequences can confer a replicative advantage; these sequences are abundant and transfer "laterally" between different memes. Subpopulations of the social network can preferentially transmit a specific variant of a meme if the variant matches their beliefs or culture. Understanding the mechanism driving change in diffusing information has important implications for how we interpret and harness the information that reaches us through our social networks.

MOTIVATION: Database searching algorithms for proteins use scoring matrices based on average protein properties, and thus are dominated by globular proteins. However, since transmembrane regions of a protein are in a distinctly different environment than globular proteins, one would expect generalized substitution matrices to be inappropriate for transmembrane regions. RESULTS: We present the PHAT (predicted hydrophobic and transmembrane) matrix, which significantly outperforms generalized matrices and a previously published transmembrane matrix in searches with transmembrane queries. We conclude that a better matrix can be constructed by using background frequencies characteristic of the twilight zone, where low-scoring true positives have scores indistinguishable from high-scoring false positives, rather than the amino acid frequencies of the database. The PHAT matrix may help improve the accuracy of sequence alignments and evolutionary trees of membrane proteins.