These tools will no longer be maintained as of December 31, 2024. Archived website can be found here. PubMed4Hh GitHub repository can be found here. Contact NLM Customer Service if you have questions.
255 related articles for article (PubMed ID: 31220250)
1. PPR-Meta: a tool for identifying phages and plasmids from metagenomic fragments using deep learning. Fang Z; Tan J; Wu S; Li M; Xu C; Xie Z; Zhu H Gigascience; 2019 Jun; 8(6):. PubMed ID: 31220250 [TBL] [Abstract][Full Text] [Related]
2. 3CAC: improving the classification of phages and plasmids in metagenomic assemblies using assembly graphs. Pu L; Shamir R Bioinformatics; 2022 Sep; 38(Suppl_2):ii56-ii61. PubMed ID: 36124804 [TBL] [Abstract][Full Text] [Related]
3. PlasGUN: gene prediction in plasmid metagenomic short reads using deep learning. Fang Z; Tan J; Wu S; Li M; Wang C; Liu Y; Zhu H Bioinformatics; 2020 May; 36(10):3239-3241. PubMed ID: 32091572 [TBL] [Abstract][Full Text] [Related]
4. DeePhage: distinguishing virulent and temperate phage-derived sequences in metavirome data with a deep learning approach. Wu S; Fang Z; Tan J; Li M; Wang C; Guo Q; Xu C; Jiang X; Zhu H Gigascience; 2021 Sep; 10(9):. PubMed ID: 34498685 [TBL] [Abstract][Full Text] [Related]
5. DeephageTP: a convolutional neural network framework for identifying phage-specific proteins from metagenomic sequencing data. Chu Y; Guo S; Cui D; Fu X; Ma Y PeerJ; 2022; 10():e13404. PubMed ID: 35698617 [TBL] [Abstract][Full Text] [Related]
6. Gauge your phage: benchmarking of bacteriophage identification tools in metagenomic sequencing data. Ho SFS; Wheeler NE; Millard AD; van Schaik W Microbiome; 2023 Apr; 11(1):84. PubMed ID: 37085924 [TBL] [Abstract][Full Text] [Related]
7. PLASMe: a tool to identify PLASMid contigs from short-read assemblies using transformer. Tang X; Shang J; Ji Y; Sun Y Nucleic Acids Res; 2023 Aug; 51(15):e83. PubMed ID: 37427782 [TBL] [Abstract][Full Text] [Related]
8. Seeker: alignment-free identification of bacteriophage genomes by deep learning. Auslander N; Gussow AB; Benler S; Wolf YI; Koonin EV Nucleic Acids Res; 2020 Dec; 48(21):e121. PubMed ID: 33045744 [TBL] [Abstract][Full Text] [Related]
9. Metagenomic assembly is the main bottleneck in the identification of mobile genetic elements. Kerkvliet JJ; Bossers A; Kers JG; Meneses R; Willems R; Schürch AC PeerJ; 2024; 12():e16695. PubMed ID: 38188174 [TBL] [Abstract][Full Text] [Related]
10. MOBFinder: a tool for mobilization typing of plasmid metagenomic fragments based on a language model. Feng T; Wu S; Zhou H; Fang Z Gigascience; 2024 Jan; 13():. PubMed ID: 39101782 [TBL] [Abstract][Full Text] [Related]
11. Accurate identification of bacteriophages from metagenomic data using Transformer. Shang J; Tang X; Guo R; Sun Y Brief Bioinform; 2022 Jul; 23(4):. PubMed ID: 35769000 [TBL] [Abstract][Full Text] [Related]
12. Bacteriophage classification for assembled contigs using graph convolutional network. Shang J; Jiang J; Sun Y Bioinformatics; 2021 Jul; 37(Suppl_1):i25-i33. PubMed ID: 34252923 [TBL] [Abstract][Full Text] [Related]
13. Phage-bacterial contig association prediction with a convolutional neural network. Tang T; Hou S; Fuhrman JA; Sun F Bioinformatics; 2022 Jun; 38(Suppl 1):i45-i52. PubMed ID: 35758806 [TBL] [Abstract][Full Text] [Related]
14. cBar: a computer program to distinguish plasmid-derived from chromosome-derived sequence fragments in metagenomics data. Zhou F; Xu Y Bioinformatics; 2010 Aug; 26(16):2051-2. PubMed ID: 20538725 [TBL] [Abstract][Full Text] [Related]
15. SCAPP: an algorithm for improved plasmid assembly in metagenomes. Pellow D; Zorea A; Probst M; Furman O; Segal A; Mizrahi I; Shamir R Microbiome; 2021 Jun; 9(1):144. PubMed ID: 34172093 [TBL] [Abstract][Full Text] [Related]
16. HOTSPOT: hierarchical host prediction for assembled plasmid contigs with transformer. Ji Y; Shang J; Tang X; Sun Y Bioinformatics; 2023 May; 39(5):. PubMed ID: 37086432 [TBL] [Abstract][Full Text] [Related]
17. PhaTYP: predicting the lifestyle for bacteriophages using BERT. Shang J; Tang X; Sun Y Brief Bioinform; 2023 Jan; 24(1):. PubMed ID: 36659812 [TBL] [Abstract][Full Text] [Related]
18. Identifying Phage Sequences From Metagenomic Data Using Deep Neural Network With Word Embedding and Attention Mechanism. Ma L; Deng W; Bai Y; Du Z; Xiao M; Wang L; Li J; Nandi AK IEEE/ACM Trans Comput Biol Bioinform; 2023; 20(6):3772-3785. PubMed ID: 37812548 [TBL] [Abstract][Full Text] [Related]
19. SourceFinder: a Machine-Learning-Based Tool for Identification of Chromosomal, Plasmid, and Bacteriophage Sequences from Assemblies. Aytan-Aktug D; Grigorjev V; Szarvas J; Clausen PTLC; Munk P; Nguyen M; Davis JJ; Aarestrup FM; Lund O Microbiol Spectr; 2022 Dec; 10(6):e0264122. PubMed ID: 36377945 [TBL] [Abstract][Full Text] [Related]
20. Identification of the conjugative and mobilizable plasmid fragments in the plasmidome using sequence signatures. Fang Z; Zhou H Microb Genom; 2020 Nov; 6(11):. PubMed ID: 33074084 [TBL] [Abstract][Full Text] [Related] [Next] [New Search]