BioSeq-BLM: a platform for analyzing DNA, RNA and protein sequences based on biological language models

Hong Liang Li; Yi He Pang; Bin Liu

doi:10.1093/nar/gkab829

BioSeq-BLM: a platform for analyzing DNA, RNA and protein sequences based on biological language models

Hong Liang Li, Yi He Pang, Bin Liu^*

^*Corresponding author for this work

School of Computer Science and Technology

Beijing Institute of Technology

Research output: Contribution to journal › Article › peer-review

137 Citations (Scopus)

Abstract

In order to uncover the meanings of ‘book of life’, 155 different biological language models (BLMs) for DNA, RNA and protein sequence analysis are discussed in this study, which are able to extract the linguistic properties of ‘book of life’. We also extend the BLMs into a system called BioSeq-BLM for automatically representing and analyzing the sequence data. Experimental results show that the predictors generated by BioSeq-BLM achieve comparable or even obviously better performance than the exiting state-of-the-art predictors published in literatures, indicating that BioSeq-BLM will provide new approaches for biological sequence analysis based on natural language processing technologies, and contribute to the development of this very important field. In order to help the readers to use BioSeq-BLM for their own experiments, the corresponding web server and stand-alone package are established and released, which can be freely accessed at http://bliulab.net/BioSeq-BLM/.

Original language	English
Pages (from-to)	E129
Journal	Nucleic Acids Research
Volume	49
Issue number	22
DOIs	https://doi.org/10.1093/nar/gkab829
Publication status	Published - 16 Dec 2021

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title = "BioSeq-BLM: a platform for analyzing DNA, RNA and protein sequences based on biological language models",

abstract = "In order to uncover the meanings of {\textquoteleft}book of life{\textquoteright}, 155 different biological language models (BLMs) for DNA, RNA and protein sequence analysis are discussed in this study, which are able to extract the linguistic properties of {\textquoteleft}book of life{\textquoteright}. We also extend the BLMs into a system called BioSeq-BLM for automatically representing and analyzing the sequence data. Experimental results show that the predictors generated by BioSeq-BLM achieve comparable or even obviously better performance than the exiting state-of-the-art predictors published in literatures, indicating that BioSeq-BLM will provide new approaches for biological sequence analysis based on natural language processing technologies, and contribute to the development of this very important field. In order to help the readers to use BioSeq-BLM for their own experiments, the corresponding web server and stand-alone package are established and released, which can be freely accessed at http://bliulab.net/BioSeq-BLM/.",

author = "Li, {Hong Liang} and Pang, {Yi He} and Bin Liu",

note = "Publisher Copyright: {\textcopyright} The Author(s) 2021. Published by Oxford University Press on behalf of Nucleic Acids Research.",

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doi = "10.1093/nar/gkab829",

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T2 - a platform for analyzing DNA, RNA and protein sequences based on biological language models

AU - Li, Hong Liang

AU - Pang, Yi He

AU - Liu, Bin

PY - 2021/12/16

Y1 - 2021/12/16

N2 - In order to uncover the meanings of ‘book of life’, 155 different biological language models (BLMs) for DNA, RNA and protein sequence analysis are discussed in this study, which are able to extract the linguistic properties of ‘book of life’. We also extend the BLMs into a system called BioSeq-BLM for automatically representing and analyzing the sequence data. Experimental results show that the predictors generated by BioSeq-BLM achieve comparable or even obviously better performance than the exiting state-of-the-art predictors published in literatures, indicating that BioSeq-BLM will provide new approaches for biological sequence analysis based on natural language processing technologies, and contribute to the development of this very important field. In order to help the readers to use BioSeq-BLM for their own experiments, the corresponding web server and stand-alone package are established and released, which can be freely accessed at http://bliulab.net/BioSeq-BLM/.

AB - In order to uncover the meanings of ‘book of life’, 155 different biological language models (BLMs) for DNA, RNA and protein sequence analysis are discussed in this study, which are able to extract the linguistic properties of ‘book of life’. We also extend the BLMs into a system called BioSeq-BLM for automatically representing and analyzing the sequence data. Experimental results show that the predictors generated by BioSeq-BLM achieve comparable or even obviously better performance than the exiting state-of-the-art predictors published in literatures, indicating that BioSeq-BLM will provide new approaches for biological sequence analysis based on natural language processing technologies, and contribute to the development of this very important field. In order to help the readers to use BioSeq-BLM for their own experiments, the corresponding web server and stand-alone package are established and released, which can be freely accessed at http://bliulab.net/BioSeq-BLM/.

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BioSeq-BLM: a platform for analyzing DNA, RNA and protein sequences based on biological language models

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