22,238 research outputs found
Near-optimal Assembly for Shotgun Sequencing with Noisy Reads
Recent work identified the fundamental limits on the information requirements
in terms of read length and coverage depth required for successful de novo
genome reconstruction from shotgun sequencing data, based on the idealistic
assumption of no errors in the reads (noiseless reads). In this work, we show
that even when there is noise in the reads, one can successfully reconstruct
with information requirements close to the noiseless fundamental limit. A new
assembly algorithm, X-phased Multibridging, is designed based on a
probabilistic model of the genome. It is shown through analysis to perform well
on the model, and through simulations to perform well on real genomes
Exploration of Reaction Pathways and Chemical Transformation Networks
For the investigation of chemical reaction networks, the identification of
all relevant intermediates and elementary reactions is mandatory. Many
algorithmic approaches exist that perform explorations efficiently and
automatedly. These approaches differ in their application range, the level of
completeness of the exploration, as well as the amount of heuristics and human
intervention required. Here, we describe and compare the different approaches
based on these criteria. Future directions leveraging the strengths of chemical
heuristics, human interaction, and physical rigor are discussed.Comment: 48 pages, 4 figure
- …