ABSTRACT
Motivation: As more and larger genomics studies appear, there is a growing need for comprehensive and queryable cross-study summaries. These enable researchers to leverage vast datasets that would otherwise be difficult to obtain. Results: Snaptron is a search engine for summarized RNA sequencing data with a query planner that leverages R-tree, B-tree and inverted indexing strategies to rapidly execute queries over 146 million exon-exon splice junctions from over 70 000 human RNA-seq samples. Queries can be tailored by constraining which junctions and samples to consider. Snaptron can score junctions according to tissue specificity or other criteria, and can score samples according to the relative frequency of different splicing patterns. We describe the software and outline biological questions that can be explored with Snaptron queries. Availability and implementation: Documentation is at http://snaptron.cs.jhu.edu. Source code is at https://github.com/ChristopherWilks/snaptron and https://github.com/ChristopherWilks/snaptron-experiments with a CC BY-NC 4.0 license. Contact: chris.wilks@jhu.edu or langmea@cs.jhu.edu. Supplementary information: Supplementary data are available at Bioinformatics online.
Subject(s)
High-Throughput Nucleotide Sequencing/methods , RNA Splicing , Sequence Analysis, RNA/methods , Software , Exons , HumansABSTRACT
We present a closed-loop adaptive optics system based on a holographic sensing method. The system uses a multiplexed holographic recording of the response functions of each actuator in a deformable mirror. By comparing the output intensity measured in a pair of photodiodes, the absolute phase can be measured over each actuator location. From this a feedback correction signal is applied to the input beam without need for a computer. The sensing and correction is applied to each actuator in parallel, so the bandwidth is independent of the number of actuator. We demonstrate a breadboard system using a 32-actuator MEMS deformable mirror capable of operating at over 10 kHz without a computer in the loop.
