ArticleInternational journal of molecular sciences2017
UltraPse: A Universal and Extensible Software Platform for Representing Biological Sequences.
Article in International journal of molecular sciences, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed.
- From nucleotides to numbers: a comprehensive review of RNA feature extraction methods for computational modelling.Briefings in bioinformatics · 2025Review
- Review of Machine Learning Methods for the Prediction and Reconstruction of Metabolic Pathways.Frontiers in molecular biosciences · 2021Review
- Use of Chou's 5-steps rule to predict the subcellular localization of gram-negative and gram-positive bacterial proteins by multi-label learning based on gene ontology annotation and profile alignment.Journal of integrative bioinformatics · 2020Article
- Identifying Heat Shock Protein Families from Imbalanced Data by Using Combined Features.Computational and mathematical methods in medicine · 2020Article
- Identification of an Individualized Prognostic Signature Based on the RWSR Model in Early-Stage Bladder Carcinoma.BioMed research international · 2020Article
- SFPEL-LPI: Sequence-based feature projection ensemble learning for predicting LncRNA-protein interactions.PLoS computational biology · 2018Article
- Special Protein Molecules Computational Identification.International journal of molecular sciences · 2018Article
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Authors and funding
5 authors.
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Abstract
With the avalanche of biological sequences in public databases, one of the most challenging problems in computational biology is to predict their biological functions and cellular attributes. Most of the existing prediction algorithms can only handle fixed-length numerical vectors. Therefore, it is important to be able to represent biological sequences with various lengths using fixed-length numerical vectors. Although several algorithms, as well as software implementations, have been developed to address this problem, these existing programs can only provide a fixed number of representation modes. Every time a new sequence representation mode is developed, a new program will be needed. In this paper, we propose the UltraPse as a universal software platform for this problem. The function of the UltraPse is not only to generate various existing sequence representation modes, but also to simplify all future programming works in developing novel representation modes. The extensibility of UltraPse is particularly enhanced. It allows the users to define their own representation mode, their own physicochemical properties, or even their own types of biological sequences. Moreover, UltraPse is also the fastest software of its kind. The source code package, as well as the executables for both Linux and Windows platforms, can be downloaded from the GitHub repository.
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