Dataset Information

Remote homology search with hidden Potts models.

ABSTRACT: Most methods for biological sequence homology search and alignment work with primary sequence alone, neglecting higher-order correlations. Recently, statistical physics models called Potts models have been used to infer all-by-all pairwise correlations between sites in deep multiple sequence alignments, and these pairwise couplings have improved 3D structure predictions. Here we extend the use of Potts models from structure prediction to sequence alignment and homology search by developing what we call a hidden Potts model (HPM) that merges a Potts emission process to a generative probability model of insertion and deletion. Because an HPM is incompatible with efficient dynamic programming alignment algorithms, we develop an approximate algorithm based on importance sampling, using simpler probabilistic models as proposal distributions. We test an HPM implementation on RNA structure homology search benchmarks, where we can compare directly to exact alignment methods that capture nested RNA base-pairing correlations (stochastic context-free grammars). HPMs perform promisingly in these proof of principle experiments.

SUBMITTER: Wilburn GW

PROVIDER: S-EPMC7728182 | biostudies-literature | 2020 Nov

REPOSITORIES: biostudies-literature

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Publications

Remote homology search with hidden Potts models.

Wilburn Grey W GW Eddy Sean R SR

PLoS computational biology 20201130 11

Most methods for biological sequence homology search and alignment work with primary sequence alone, neglecting higher-order correlations. Recently, statistical physics models called Potts models have been used to infer all-by-all pairwise correlations between sites in deep multiple sequence alignments, and these pairwise couplings have improved 3D structure predictions. Here we extend the use of Potts models from structure prediction to sequence alignment and homology search by developing what ...[more]

PMID: 33253143

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Project description:The results of two experiments are analyzed to find out how artistic expertise influences visual search. Experiment I comprised survey data of 1,065 students on self-reported visual memory skills and their ability to find three targets in four images of artwork. Experiment II comprised eye movement data of 50 Visual Literacy (VL) experts and non-experts whose eye movements during visual search were analyzed for nine images of artwork as an external validation of the assessment tasks performed in Sample I. No time constraint was set for completion of the visual search task. A latent profile analysis revealed four typical solution patterns for the students in Sample I, including a mainstream group, a group that completes easy images fast and difficult images slowly, a fast and erroneous group, and a slow working student group, depending on task completion time and on the probability of finding all three targets. Eidetic memory, performance in art education and visual imagination as self-reported visual skills have significant impact on latent class membership probability. We present a hidden Markov model (HMM) approach to uncover underlying regions of attraction that result from visual search eye-movement behavior in Experiment II. VL experts and non-experts did not significantly differ in task time and number of targets found but they did differ in their visual search process: compared to non-experts, experts showed greater precision in fixating specific prime and target regions, assessed through hidden state fixation overlap. Exploratory analysis of HMMs revealed differences between experts and non-experts in image locations of attraction (HMM states). Experts seem to focus their attention on smaller image parts whereas non-experts used wider parts of the image during their search. Differences between experts and non-experts depend on the relative saliency of targets embedded in images. HMMs can determine the effect of expertise on exploratory eye movements executed during visual search tasks. Further research on HMMs and art expertise is required to confirm exploratory results.

Dataset Information

Remote homology search with hidden Potts models.

Publications

Remote homology search with hidden Potts models.

Similar Datasets

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