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

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 Bio...

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Published in:Nucleic acids research Vol. 49; no. 22; p. e129
Main Authors: Li, Hong-Liang, Pang, Yi-He, Liu, Bin
Format: Journal Article
Language:English
Published: England Oxford University Press 16.12.2021
Subjects:
Deoxyribonuclease I
DNA-Binding Proteins - chemistry
Intrinsically Disordered Proteins - chemistry
Methods Online
MicroRNAs - chemistry
Models, Statistical
Natural Language Processing
Nucleic Acid Conformation
RNA Precursors - chemistry
RNA-Binding Proteins - chemistry
Sequence Analysis, DNA - methods
Sequence Analysis, Protein - methods
Sequence Analysis, RNA - methods
Software
ISSN:0305-1048, 1362-4962, 1362-4962
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Abstract 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/.
AbstractList 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/.
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/.
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/.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/.
Author Li, Hong-Liang
Pang, Yi-He
Liu, Bin
Author_xml – sequence: 1
  givenname: Hong-Liang
  surname: Li
  fullname: Li, Hong-Liang
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– sequence: 2
  givenname: Yi-He
  surname: Pang
  fullname: Pang, Yi-He
– sequence: 3
  givenname: Bin
  orcidid: 0000-0003-3685-9469
  surname: Liu
  fullname: Liu, Bin
  email: bliu@bliulab.net
BackLink https://www.ncbi.nlm.nih.gov/pubmed/34581805$$D View this record in MEDLINE/PubMed
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Snippet 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...
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...
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...
SourceID pubmedcentral
proquest
pubmed
crossref
oup
SourceType Open Access Repository
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Index Database
Enrichment Source
Publisher
StartPage e129
SubjectTerms Deoxyribonuclease I
DNA-Binding Proteins - chemistry
Intrinsically Disordered Proteins - chemistry
Methods Online
MicroRNAs - chemistry
Models, Statistical
Natural Language Processing
Nucleic Acid Conformation
RNA Precursors - chemistry
RNA-Binding Proteins - chemistry
Sequence Analysis, DNA - methods
Sequence Analysis, Protein - methods
Sequence Analysis, RNA - methods
Software
Title BioSeq-BLM: a platform for analyzing DNA, RNA and protein sequences based on biological language models
URI https://www.ncbi.nlm.nih.gov/pubmed/34581805
https://www.proquest.com/docview/2577458303
https://pubmed.ncbi.nlm.nih.gov/PMC8682797
Volume 49
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