BioSeq-Analysis2.0: an updated platform for analyzing DNA, RNA and protein sequences at sequence level and residue level based on machine learning approaches

By Bin Liu, Xin Gao, Han Zhang. Nucleic Acids Research, 2019

354 citations recorded by the source corpus.

Abstract As the first web server to analyze various biological sequences at sequence level based on machine learning approaches, many powerful predictors in the field of computational biology have been developed with the assistance of the BioSeq-Analysis. However, the BioSeq-Analysis can be only applied to the sequence-level analysis tasks, preventing its applications to the residue-level analysis tasks, and an intelligent tool that is able to automatically generate various predictors for biological sequence analysis at both residue level and sequence level is highly desired. In this regard, we decided to publish an important updated server covering a total of 26 features at the residue level and 90 features at the sequence level called BioSeq-Analysis2.0 (http://bliulab.net/BioSeq-Analysis2.0/), by which the users only need to upload the benchmark dataset, and the BioSeq-Analysis2.0 can generate the predictors for both residue-level analysis and sequence-level analysis tasks. Furthermore, the corresponding stand-alone tool was also provided, which can be downloaded from http://bliulab.net/BioSeq-Analysis2.0/download/. To the best of our knowledge, the BioSeq-Analysis2.0 is the first tool for generating predictors for biological sequence analysis tasks at residue level. Specifically, the experimental results indicated that the predictors developed by BioSeq-Analysis2.0 can achieve comparable or even better performance than the existing state-of-the-art predictors.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/4a59c3aaffd4af7196b10f9e6c0e04b8c73c5cd6

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In Molecular Biology

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Citations in the corpus

• ProtGPT2 is a deep unsupervised language model for protein design (2022, methodology): “A remarkable collection of supervised language models applied to bio-molecules is available in the BioSeq-BLM platform 5,6 .”
• SBSM-Pro: support bio-sequence machine for proteins (2023, neutral): “This led to the emergence of platforms that combine feature extraction and classifiers, such as gkmSVM [15], iLearnPlus [16], Biological Seq-Analysis 2.0 [17], and BioSeq-BLM [18].”