VFM: Identification of Bacteriophages From Metagenomic Bins and Contigs Based on Features Related to Gene and Genome Composition
As the main regulator of microbial community composition, bacteriophages exist widely on Earth. However, since they are hidden in metagenomes, most of them are unknown. To identify phages from metagenomes more effectively, a new tool named VFM (Virus Finding & Mining) is presented in this pa...
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doaj-d5492e383afd458087aff33081fb829d2021-03-29T22:59:15ZengIEEEIEEE Access2169-35362019-01-01717752917753810.1109/ACCESS.2019.29578338924706VFM: Identification of Bacteriophages From Metagenomic Bins and Contigs Based on Features Related to Gene and Genome CompositionQiaoliang Liu0https://orcid.org/0000-0002-6832-3223Fu Liu1Jiaxue He2Miaolei Zhou3https://orcid.org/0000-0002-8040-2768Tao Hou4Yun Liu5College of Communication Engineering, Jilin University, Changchun, ChinaCollege of Communication Engineering, Jilin University, Changchun, ChinaGenetic Diagnosis Center, The First Hospital of Jilin University, Changchun, ChinaCollege of Communication Engineering, Jilin University, Changchun, ChinaCollege of Communication Engineering, Jilin University, Changchun, ChinaCollege of Communication Engineering, Jilin University, Changchun, ChinaAs the main regulator of microbial community composition, bacteriophages exist widely on Earth. However, since they are hidden in metagenomes, most of them are unknown. To identify phages from metagenomes more effectively, a new tool named VFM (Virus Finding & Mining) is presented in this paper. VFM has two versions, i.e., bin-VFM and unbin-VFM. Eighteen new features describing the codon usage bias, the proportion of hits of clusters of orthologous groups of proteins (COG), and 1-mer and 2-mer frequency are introduced to improve the performance of the classifiers. By using missing value interpolation, bin-VFM improves the classification performance for short sequence bins significantly. Compared with previous tools for virus mining, bin-VFM and unbin-VFM perform much better for simulated and real metagenomes with short and long sequences respectively. Thus, VFM may play a helpful role in studies of metagenome-related problems, such as horizontal gene transfer and antibiotic resistance. VFM is freely available at https://github.com/liuql2019/VFM.https://ieeexplore.ieee.org/document/8924706/Codon usage biasCOGmissing value interpolationmetagenomic virusesphage miningshort k-mer frequency |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Qiaoliang Liu Fu Liu Jiaxue He Miaolei Zhou Tao Hou Yun Liu |
spellingShingle |
Qiaoliang Liu Fu Liu Jiaxue He Miaolei Zhou Tao Hou Yun Liu VFM: Identification of Bacteriophages From Metagenomic Bins and Contigs Based on Features Related to Gene and Genome Composition IEEE Access Codon usage bias COG missing value interpolation metagenomic viruses phage mining short k-mer frequency |
author_facet |
Qiaoliang Liu Fu Liu Jiaxue He Miaolei Zhou Tao Hou Yun Liu |
author_sort |
Qiaoliang Liu |
title |
VFM: Identification of Bacteriophages From Metagenomic Bins and Contigs Based on Features Related to Gene and Genome Composition |
title_short |
VFM: Identification of Bacteriophages From Metagenomic Bins and Contigs Based on Features Related to Gene and Genome Composition |
title_full |
VFM: Identification of Bacteriophages From Metagenomic Bins and Contigs Based on Features Related to Gene and Genome Composition |
title_fullStr |
VFM: Identification of Bacteriophages From Metagenomic Bins and Contigs Based on Features Related to Gene and Genome Composition |
title_full_unstemmed |
VFM: Identification of Bacteriophages From Metagenomic Bins and Contigs Based on Features Related to Gene and Genome Composition |
title_sort |
vfm: identification of bacteriophages from metagenomic bins and contigs based on features related to gene and genome composition |
publisher |
IEEE |
series |
IEEE Access |
issn |
2169-3536 |
publishDate |
2019-01-01 |
description |
As the main regulator of microbial community composition, bacteriophages exist widely on Earth. However, since they are hidden in metagenomes, most of them are unknown. To identify phages from metagenomes more effectively, a new tool named VFM (Virus Finding & Mining) is presented in this paper. VFM has two versions, i.e., bin-VFM and unbin-VFM. Eighteen new features describing the codon usage bias, the proportion of hits of clusters of orthologous groups of proteins (COG), and 1-mer and 2-mer frequency are introduced to improve the performance of the classifiers. By using missing value interpolation, bin-VFM improves the classification performance for short sequence bins significantly. Compared with previous tools for virus mining, bin-VFM and unbin-VFM perform much better for simulated and real metagenomes with short and long sequences respectively. Thus, VFM may play a helpful role in studies of metagenome-related problems, such as horizontal gene transfer and antibiotic resistance. VFM is freely available at https://github.com/liuql2019/VFM. |
topic |
Codon usage bias COG missing value interpolation metagenomic viruses phage mining short k-mer frequency |
url |
https://ieeexplore.ieee.org/document/8924706/ |
work_keys_str_mv |
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