HCV sequence database statistics

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Number of citations per year for the bioinformatics software tool HCV sequence database
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Protocols

HCV sequence database specifications

Information


Unique identifier OMICS_03070
Name HCV sequence database
Restrictions to use None
Maintained Yes

Taxon


  • Viruses
    • Hepatitis C virus genotype 2
    • Hepatitis C virus genotype 3
    • Hepatitis C virus genotype 4

Maintainer


  • person_outline HCV sequence database Team

Publication for HCV sequence database

HCV sequence database citations

 (17)
library_books

Know Your Enemy: Successful Bioinformatic Approaches to Predict Functional RNA Structures in Viral RNAs

2018
Front Microbiol
PMCID: 5758548
PMID: 29354101
DOI: 10.3389/fmicb.2017.02582

[…] onstraints could also be due to primary sequence conservation in RNA (or DNA).Alternatively, codon-based alignment could have been be done using webPRANK (Löytynoja and Goldman, ) or Codon Alignment (HCV sequence database; Kuiken et al., ). Significant synonymous constraint sites of aligned CDS can also be detected using FRESco (Sealfon et al., ) or synplot2 (Firth, ). Many automated alignments of […]

call_split

Rebound of Cotton leaf curl Multan virus and its exclusive detection in cotton leaf curl disease outbreak, Punjab (India), 2015

2017
Sci Rep
PMCID: 5727119
PMID: 29234082
DOI: 10.1038/s41598-017-17680-9
call_split See protocol

[…] ers provided in the relevant recent literature,,,,. To save computational time, redundant sequences were sorted out by running the datasets through the ElimDupes program implemented in the Los Alamos HCV sequence database server (https://hcv.lanl.gov/content/sequence/ELIMDUPES/elimdupes.html) and sequences representing a group of identical or near identical sequences (percent nucleotide identity, […]

library_books

Detection of Natural Resistance Associated Substitutions by Ion Semiconductor Technology in HCV1b Positive, Direct Acting Antiviral Agents Naïve Patients

2016
Int J Mol Sci
PMCID: 5037695
PMID: 27618896
DOI: 10.3390/ijms17091416

[…] g Tool v.2.0 [] and the COMET HCV typing tool [], and were also used in a maximum likelihood phylogenetic inference incorporating reference sequences available from the Los Alamos National Laboratory HCV Sequence Database () []. Sequences were aligned with Clustal W [] and manually edited in MEGA v.5.2.2 []. Trees were estimated, inferring with the generalized time reversible (GTR) nucleotide subs […]

library_books

Reconstitution and Functional Analysis of a Full Length Hepatitis C Virus NS5B Polymerase on a Supported Lipid Bilayer

2016
PMCID: 4965852
PMID: 27504492
DOI: 10.1021/acscentsci.6b00112

[…] An alignment of the nucleotides surrounding the AUG start codon in domain IV of the HCV IRES was performed using all 471 sequences from the Los Alamos HCV Sequence Database. Weblogo (http://weblogo.berkeley.edu/) was used to generate the sequence alignment display in A. […]

call_split

The Molecular Epidemiological Study of HCV Subtypes among Intravenous Drug Users and Non Injection Drug Users in China

2015
PLoS One
PMCID: 4605846
PMID: 26466103
DOI: 10.1371/journal.pone.0140263
call_split See protocol

[…] We used ChromasPro 1.5 to trim and assemble sequences. Then we used BioEdit 4.0 to perform multiple alignments against the NS5B reference sequences from the HCV Sequence Database (https://hcv.lanl.gov/content/sequence/HCV/ToolsOutline.html). Finally, we ran Mega 4.0 to conduct the phylogenetic analyses. Subtype information was read from the resulting phyl […]

library_books

Genetic Diversity and Selective Pressure in Hepatitis C Virus Genotypes 1–6: Significance for Direct Acting Antiviral Treatment and Drug Resistance

2015
Viruses
PMCID: 4584301
PMID: 26389941
DOI: 10.3390/v7092857

[…] Full-length HCV genome nucleotide sequences were downloaded from the Los Alamos National Laboratory (LANL) HCV Sequence Database (http://hcv.lanl.gov) [], resulting in a dataset of 1631 sequences of HCV genotypes 1–6. Genotype 7 was excluded from the analysis, as only one full-length sequence was available […]


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HCV sequence database institution(s)
HCV database, Los Alamos National Laboratory, Los Alamos, NM, USA

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