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Protocols

ViroBLAST specifications

Information


Unique identifier OMICS_26702
Name ViroBLAST
Interface Web user interface
Restrictions to use None
Input data Some query sequences.
Input format FASTA
Computer skills Basic
Version 2.6+
Stability Stable
Maintained Yes

Maintainers


  • person_outline James Mullins
  • person_outline ViroBLAST Team

Additional information


https://indra.mullins.microbiol.washington.edu/viroblast/docs/viroblasthelp.html

Information


Unique identifier OMICS_26702
Name ViroBLAST
Software type Application/Script
Interface Command line interface
Restrictions to use License purchase required
Operating system Unix/Linux, Mac OS
Computer skills Advanced
Stability Stable
Maintained Yes

Download


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Versioning


No version available

Maintainers


  • person_outline James Mullins
  • person_outline ViroBLAST Team

Additional information


https://indra.mullins.microbiol.washington.edu/viroblast/docs/viroblasthelp.html

Publication for ViroBLAST

ViroBLAST citations

 (58)
library_books

AmpuBase: a transcriptome database for eight species of apple snails (Gastropoda: Ampullariidae)

2018
BMC Genomics
PMCID: 5839033
PMID: 29506476
DOI: 10.1186/s12864-018-4553-9

[…] and KEGG search pages are integrated. In brief, for each species, a relational database was developed using MySQL v5.6.34 and hosted on an Apache HTTP server. The BLAST search function is powered by ViroBLAST [] using the PHP programming language. The database consists of DNA and protein sequences of all unigenes that are linked with associated NCBI nr, GO and KEGG annotations through unigene ID. […]

library_books

ASGDB: a specialised genomic resource for interpreting Anopheles sinensis insecticide resistance

2018
PMCID: 5763776
PMID: 29321052
DOI: 10.1186/s13071-017-2584-8

[…] lizing genes with large-scale sequence datasets [, ]. This next generation AJAX-based genome browser, built with JavaScript and HTML5, enables fast and smooth animated genome navigation over the web. ViroBLAST has also been integrated into the ASGDB system []. The interface of “Resistance surveillance” utilizes OpenLayers 3 (high-performance, feature-packed web mapping library) to visualize the da […]

library_books

Impact of the 7 bp deletion in HvGA20ox2 gene on agronomic important traits in barley (Hordeum vulgare L.)

2017
BMC Plant Biol
PMCID: 5688404
PMID: 29143605
DOI: 10.1186/s12870-017-1121-4

[…] ove that Barke is the sdw1.d mutant we re-sequenced the exon 1 of HvGA20ox2 gene for the barley variety. To design primers we aligned the morex_contig_40861 (http://webblast.ipk-gatersleben.de/barley/viroblast.php) containing the published fragment of HvGA20ox2 sequence and MLOC_56462.1 that is the coding sequence for HvGA20ox2 gene (Fig. ). The PCR fragment of 488 bp was successfully amplified an […]

library_books

Association mapping of drought tolerance related traits in barley to complement a traditional biparental QTL mapping study

2017
PMCID: 5750332
PMID: 29071393
DOI: 10.1007/s00122-017-2994-1

[…] The physical positions of markers within the QTL regions for drought tolerance in spring barley (Wójcik-Jagła et al. ) were identified using the ViroBLAST program (Deng et al. ) and genome sequence databases for Morex, Barke, and Bowman cultivars as references. The marker sequences most similar to the contig sequence were considered. Based on […]

call_split

Patterns and rates of viral evolution in HIV 1 subtype B infected females and males

2017
PLoS One
PMCID: 5646779
PMID: 29045410
DOI: 10.1371/journal.pone.0182443
call_split See protocol

[…] n room absent of any PCR-amplified or plasmid DNA, and all gag and env-gp120 sequence assemblies were regularly compared against the continually updated Mullins laboratory HIV sequence database using ViroBLAST [] [http://indra.mullins.microbiol.washington.edu/viroblast/viroblast.php]. As it is particularly difficult to detect specimen mix-up or contamination in longitudinal studies, researchers al […]

library_books

HIV 1 transmission networks in high risk fishing communities on the shores of Lake Victoria in Uganda: A phylogenetic and epidemiological approach

2017
PLoS One
PMCID: 5638258
PMID: 29023474
DOI: 10.1371/journal.pone.0185818

[…] Subtype reference sequences of HIV-1 group M from the Los Alamos Sequence database [], were used to automatically align the generated sequences using ClustalX []. The software ViroBLAST was used to scan public databases for sequences similar (bootstrap ≥95%) to our sequences and for checking contamination []. We further used ElimDupes software to compare the ViroBLAST, subt […]

Citations

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ViroBLAST institution(s)
Department of Microbiology, University of Washington School of Medicine, Seattle, WA, USA
ViroBLAST funding source(s)
Supported by funds from Advanced Technology Initiative in Infectious Diseases at University of Washington and US Public Health Service grants (AI047734, AI57005, AI058894) as well as the University of Washington Center for AIDS Research (AI27757).

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