Matches in SemOpenAlex for { <https://semopenalex.org/work/W4386212812> ?p ?o ?g. }
- W4386212812 endingPage "e1011422" @default.
- W4386212812 startingPage "e1011422" @default.
- W4386212812 abstract "The study of viral communities has revealed the enormous diversity and impact these biological entities have on various ecosystems. These observations have sparked widespread interest in developing computational strategies that support the comprehensive characterisation of viral communities based on sequencing data. Here we introduce VIRify, a new computational pipeline designed to provide a user-friendly and accurate functional and taxonomic characterisation of viral communities. VIRify identifies viral contigs and prophages from metagenomic assemblies and annotates them using a collection of viral profile hidden Markov models (HMMs). These include our manually-curated profile HMMs, which serve as specific taxonomic markers for a wide range of prokaryotic and eukaryotic viral taxa and are thus used to reliably classify viral contigs. We tested VIRify on assemblies from two microbial mock communities, a large metagenomics study, and a collection of publicly available viral genomic sequences from the human gut. The results showed that VIRify could identify sequences from both prokaryotic and eukaryotic viruses, and provided taxonomic classifications from the genus to the family rank with an average accuracy of 86.6%. In addition, VIRify allowed the detection and taxonomic classification of a range of prokaryotic and eukaryotic viruses present in 243 marine metagenomic assemblies. Finally, the use of VIRify led to a large expansion in the number of taxonomically classified human gut viral sequences and the improvement of outdated and shallow taxonomic classifications. Overall, we demonstrate that VIRify is a novel and powerful resource that offers an enhanced capability to detect a broad range of viral contigs and taxonomically classify them." @default.
- W4386212812 created "2023-08-29" @default.
- W4386212812 creator A5002436511 @default.
- W4386212812 creator A5005624489 @default.
- W4386212812 creator A5025120130 @default.
- W4386212812 creator A5032901794 @default.
- W4386212812 creator A5038373632 @default.
- W4386212812 creator A5041475009 @default.
- W4386212812 creator A5062712572 @default.
- W4386212812 creator A5082240217 @default.
- W4386212812 date "2023-08-28" @default.
- W4386212812 modified "2023-09-30" @default.
- W4386212812 title "VIRify: An integrated detection, annotation and taxonomic classification pipeline using virus-specific protein profile hidden Markov models" @default.
- W4386212812 cites W1514768507 @default.
- W4386212812 cites W1966912927 @default.
- W4386212812 cites W1972708645 @default.
- W4386212812 cites W1997027215 @default.
- W4386212812 cites W2020301105 @default.
- W4386212812 cites W2040416009 @default.
- W4386212812 cites W2044530165 @default.
- W4386212812 cites W2074955520 @default.
- W4386212812 cites W2084814249 @default.
- W4386212812 cites W2085926377 @default.
- W4386212812 cites W2107282968 @default.
- W4386212812 cites W2107772251 @default.
- W4386212812 cites W2109867978 @default.
- W4386212812 cites W2119859604 @default.
- W4386212812 cites W2142678031 @default.
- W4386212812 cites W2143485490 @default.
- W4386212812 cites W2154760096 @default.
- W4386212812 cites W2156125289 @default.
- W4386212812 cites W2157678804 @default.
- W4386212812 cites W2161251845 @default.
- W4386212812 cites W2169899471 @default.
- W4386212812 cites W2277953252 @default.
- W4386212812 cites W2291003811 @default.
- W4386212812 cites W2345791363 @default.
- W4386212812 cites W2410580207 @default.
- W4386212812 cites W2464076762 @default.
- W4386212812 cites W2504173038 @default.
- W4386212812 cites W2514983714 @default.
- W4386212812 cites W2521169042 @default.
- W4386212812 cites W2526038422 @default.
- W4386212812 cites W2545536333 @default.
- W4386212812 cites W2599417231 @default.
- W4386212812 cites W2605897695 @default.
- W4386212812 cites W2732139758 @default.
- W4386212812 cites W2781754262 @default.
- W4386212812 cites W2785587412 @default.
- W4386212812 cites W2793461621 @default.
- W4386212812 cites W2806336739 @default.
- W4386212812 cites W2883002901 @default.
- W4386212812 cites W2886112809 @default.
- W4386212812 cites W2904384071 @default.
- W4386212812 cites W2913972921 @default.
- W4386212812 cites W2915659430 @default.
- W4386212812 cites W2918063357 @default.
- W4386212812 cites W2926100178 @default.
- W4386212812 cites W2927961455 @default.
- W4386212812 cites W2940459311 @default.
- W4386212812 cites W2942002471 @default.
- W4386212812 cites W2943223175 @default.
- W4386212812 cites W2949831026 @default.
- W4386212812 cites W2950044547 @default.
- W4386212812 cites W2951912016 @default.
- W4386212812 cites W2955167895 @default.
- W4386212812 cites W2977180444 @default.
- W4386212812 cites W2979358136 @default.
- W4386212812 cites W2984894304 @default.
- W4386212812 cites W2995649573 @default.
- W4386212812 cites W3003110834 @default.
- W4386212812 cites W3003557640 @default.
- W4386212812 cites W3017386511 @default.
- W4386212812 cites W3025757981 @default.
- W4386212812 cites W3028083463 @default.
- W4386212812 cites W3033129278 @default.
- W4386212812 cites W3095583226 @default.
- W4386212812 cites W3097008984 @default.
- W4386212812 cites W3118048495 @default.
- W4386212812 cites W3127656915 @default.
- W4386212812 cites W3132890345 @default.
- W4386212812 cites W3151578668 @default.
- W4386212812 cites W3167099859 @default.
- W4386212812 cites W3187038707 @default.
- W4386212812 cites W4200448990 @default.
- W4386212812 cites W4205698576 @default.
- W4386212812 cites W4239871258 @default.
- W4386212812 cites W4246297253 @default.
- W4386212812 cites W4282936970 @default.
- W4386212812 cites W4294920833 @default.
- W4386212812 cites W4309669576 @default.
- W4386212812 cites W4317716348 @default.
- W4386212812 cites W4365136917 @default.
- W4386212812 cites W4366742305 @default.
- W4386212812 cites W4378212528 @default.
- W4386212812 doi "https://doi.org/10.1371/journal.pcbi.1011422" @default.
- W4386212812 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/37639475" @default.
- W4386212812 hasPublicationYear "2023" @default.