MOTIVATION: RNA secondary structure prediction is widely used to understand RNA function. Recently, there has been a shift away from the classical minimum free energy methods to partition function-based methods that account for folding ensembles and can therefore estimate structure and base pair probabilities. However, the classical partition function algorithm scales cubically with sequence length, and is therefore prohibitively slow for long sequences. This slowness is even more severe than cubic-time free energy minimization due to a substantially larger constant factor in runtime. RESULTS: Inspired by the success of our recent LinearFold algorithm that predicts the approximate minimum free energy structure in linear time, we design a similar linear-time heuristic algorithm, LinearPartition, to approximate the partition function and base-pairing probabilities, which is shown to be orders of magnitude faster than Vienna RNAfold and CONTRAfold (e.g. 2.5 days versus 1.3 min on a sequence with length 32 753 nt). More interestingly, the resulting base-pairing probabilities are even better correlated with the ground-truth structures. LinearPartition also leads to a small accuracy improvement when used for downstream structure prediction on families with the longest length sequences (16S and 23S rRNAs), as well as a substantial improvement on long-distance base pairs (500+ nt apart). AVAILABILITY AND IMPLEMENTATION: Code: http://github.com/LinearFold/LinearPartition; Server: http://linearfold.org/partition. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Raw lines of code (LOC) is a metric that does not, at first glance, seem extremely useful for automated test generation. It is both highly language-dependent and not extremely meaningful, semantically, within a language: one coder can produce the same effect with many fewer lines than another. However, relative LOC , between components of the same project, turns out to be a highly useful metric for automated testing. In this article, we make use of a heuristic based on LOC counts for tested functions to dramatically improve the effectiveness of automated test generation. This approach is particularly valuable in languages where collecting code coverage data to guide testing has a very high overhead. We apply the heuristic to property-based Python testing using the TSTL (Template Scripting Testing Language) tool. In our experiments, the simple LOC heuristic can improve branch and statement coverage by large margins (often more than 20%, up to 40% or more) and improve fault detection by an even larger margin (usually more than 75% and up to 400% or more). The LOC heuristic is also easy to combine with other approaches and is comparable to, and possibly more effective than, two well-established approaches for guiding random testing.

MOTIVATION: Predicting the secondary structure of an ribonucleic acid (RNA) sequence is useful in many applications. Existing algorithms [based on dynamic programming] suffer from a major limitation: their runtimes scale cubically with the RNA length, and this slowness limits their use in genome-wide applications. RESULTS: We present a novel alternative O(n3)-time dynamic programming algorithm for RNA folding that is amenable to heuristics that make it run in O(n) time and O(n) space, while producing a high-quality approximation to the optimal solution. Inspired by incremental parsing for context-free grammars in computational linguistics, our alternative dynamic programming algorithm scans the sequence in a left-to-right (5'-to-3') direction rather than in a bottom-up fashion, which allows us to employ the effective beam pruning heuristic. Our work, though inexact, is the first RNA folding algorithm to achieve linear runtime (and linear space) without imposing constraints on the output structure. Surprisingly, our approximate search results in even higher overall accuracy on a diverse database of sequences with known structures. More interestingly, it leads to significantly more accurate predictions on the longest sequence families in that database (16S and 23S Ribosomal RNAs), as well as improved accuracies for long-range base pairs (500+ nucleotides apart), both of which are well known to be challenging for the current models. AVAILABILITY AND IMPLEMENTATION: Our source code is available at https://github.com/LinearFold/LinearFold, and our webserver is at http://linearfold.org (sequence limit: 100 000nt). SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.