RNA secondary structure prediction from multi-aligned sequences

It has been well accepted that the RNA secondary structures of most functional non-coding RNAs (ncRNAs) are closely related to their functions and are conserved during evolution. Hence, prediction of conserved secondary structures from evolutionarily related sequences is one important task in RNA bioinformatics; the methods are useful not only to further functional analyses of ncRNAs but also to improve the accuracy of secondary structure predictions and to find novel functional RNAs from the genome. In this review, I focus on common secondary structure prediction from a given aligned RNA sequence, in which one secondary structure whose length is equal to that of the input alignment is predicted. I systematically review and classify existing tools and algorithms for the problem, by utilizing the information employed in the tools and by adopting a unified viewpoint based on maximum expected gain (MEG) estimators. I believe that this classification will allow a deeper understanding of each tool and provide users with useful information for selecting tools for common secondary structure predictions.Comment: A preprint of an invited review manuscript that will be published in a chapter of the book `Methods in Molecular Biology'. Note that this version of the manuscript may differ from the published versio

Cross-lingual Word Clusters for Direct Transfer of Linguistic Structure

It has been established that incorporating word cluster features derived from large unlabeled corpora can significantly improve prediction of linguistic structure. While previous work has focused primarily on English, we extend these results to other languages along two dimensions. First, we show that these results hold true for a number of languages across families. Second, and more interestingly, we provide an algorithm for inducing cross-lingual clusters and we show that features derived from these clusters significantly improve the accuracy of cross-lingual structure prediction. Specifically, we show that by augmenting direct-transfer systems with cross-lingual cluster features, the relative error of delexicalized dependency parsers, trained on English treebanks and transferred to foreign languages, can be reduced by up to 13%. When applying the same method to direct transfer of named-entity recognizers, we observe relative improvements of up to 26%

Token and Type Constraints for Cross-Lingual Part-of-Speech Tagging

We consider the construction of part-of-speech taggers for resource-poor languages. Recently, manually constructed tag dictionaries from Wiktionary and dictionaries projected via bitext have been used as type constraints to overcome the scarcity of annotated data in this setting. In this paper, we show that additional token constraints can be projected from a resource-rich source language to a resource-poor target language via word-aligned bitext. We present several models to this end; in particular a partially observed conditional random field model, where coupled token and type constraints provide a partial signal for training. Averaged across eight previously studied Indo-European languages, our model achieves a 25% relative error reduction over the prior state of the art. We further present successful results on seven additional languages from different families, empirically demonstrating the applicability of coupled token and type constraints across a diverse set of languages

Distributed Many-to-Many Protein Sequence Alignment using Sparse Matrices

Identifying similar protein sequences is a core step in many computational biology pipelines such as detection of homologous protein sequences, generation of similarity protein graphs for downstream analysis, functional annotation and gene location. Performance and scalability of protein similarity searches have proven to be a bottleneck in many bioinformatics pipelines due to increases in cheap and abundant sequencing data. This work presents a new distributed-memory software, PASTIS. PASTIS relies on sparse matrix computations for efficient identification of possibly similar proteins. We use distributed sparse matrices for scalability and show that the sparse matrix infrastructure is a great fit for protein similarity searches when coupled with a fully-distributed dictionary of sequences that allows remote sequence requests to be fulfilled. Our algorithm incorporates the unique bias in amino acid sequence substitution in searches without altering the basic sparse matrix model, and in turn, achieves ideal scaling up to millions of protein sequences.Comment: To appear in International Conference for High Performance Computing, Networking, Storage, and Analysis (SC'20

Laser trapping microchip for biotechnological applications: design and development

This work presents a novel approach towards integrated dual-beam optical trapping achieved using planar lightwave circuit (PLC) technology. Three fabrication technologies sol-gel, photolithography and reactive ion etching were combined to fabricate a Laser Trapping Microchip (LTM) allowing one-dimensional manipulation of transparent micrometer-size spherical objects. Detailed steps of the LTM development are described, beginning with a theoretical approach and numerical simulations through the design and synthesis of a suitable photopatternable sol-gel material, culminating in the fabrication process and experimental confirmation of the trapping properties of the device. The proof of concept of this unique device was achieved by demonstrating its optical trapping abilities using micrometer size polystyrene beads with diameters in the range between 4 pm and 10 pm and the refractive index of 1 59. The LTM device possesses many advantages over currently existing dual-beam laser trapping systems such as small overall dimensions (~15 x 30 x 0 5 mm), low power optical power consumption (<15mW), improved stability of the optical trap due to precise alignment of the optical paths and a relatively easy fabrication process. For these reasons there are many potential applications of the LTM device in biotechnology, microfluidics and other sciences making it an attractive device for commercial use