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Associated diseases

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HostPhinder specifications

Information


Unique identifier OMICS_19863
Name HostPhinder
Interface Web user interface
Restrictions to use None
Input data A sequence.
Input format FASTA
Programming languages Python, Shell (Bash)
Computer skills Basic
Version 1.1
Stability Stable
Maintained Yes

Maintainers


  • person_outline Mette V. Larsen <>
  • person_outline Julia Villarroel <>

Information


Unique identifier OMICS_19863
Name HostPhinder
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainers


  • person_outline Mette V. Larsen <>
  • person_outline Julia Villarroel <>

Publication for HostPhinder

HostPhinder in publications

 (3)
PMCID: 5704599
PMID: 29179741
DOI: 10.1186/s40168-017-0374-3

[…] populations were defined as having at least 15% coverage in 80% or more of the rumen viral metagenomes. since none of the core populations had homology to known viruses, hosts were inferred using hostphinder [] , core viral populations were defined as having at least 15% coverage in 80% or more of the rumen viral metagenomes. since none of the core populations had homology to known viruses, […]

PMCID: 5707535
PMID: 29099783
DOI: 10.3390/v9110328

[…] for bins containing more than one contig, a weighted ani average was calculated as (2)ani¯=∑i=1nanii*li∑i=1nli where n is the number of contigs in the bin and l is the length of the member contigs. hostphinder [] was used to predict the bacterial host of the draft genomes. hostphinder predicts the host of a phage genome sequence by searching for overlapping 16-mers between the query […]

PMCID: 5427195
PMID: 28495760
DOI: 10.1128/genomeA.00110-17

[…] paired-end libraries and 30× coverage. the raw reads were assembled using the a5 pipeline (). phaster () and phispy () identified prophage regions. rast () annotated the phage-like plasmid, while hostphinder1.1 () and trnascan () identified the host range of the phage-like plasmid and trna genes, respectively., the complete sequence of the phage-like plasmid from s. derby, designated anco3, […]


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HostPhinder institution(s)
Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark; Instituto de Investigaciones Biotecnológicas, Universidad de San Martín, San Martín, Argentina
HostPhinder funding source(s)
Supported by the Center for Genomic Epidemiology at the Technical University of Denmark and funded by grant 09-067103/DSF from the Danish Council for Strategic Research, grant nr. 14-3056 from Oticon Fonden and grant 14-70-0955 from Otto Moensted Fonden.

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