Align-GVGD protocols

Align-GVGD specifications

Information


Unique identifier OMICS_00125
Name Align-GVGD
Interface Web user interface
Restrictions to use None
Input data List of mutations, MSA
Input format Text, FASTA
Programming languages Perl
Computer skills Basic
Stability Stable
Maintained Yes

Taxon


  • Primates
    • Homo sapiens

Maintainer


  • person_outline Sean V. Tavtigian <>

Publication for Align-GVGD

Align-GVGD IN pipelines

 (2)
2017
PMCID: 5800345
PMID: 28993434
DOI: 10.1136/jmedgenet-2017-104947

[…] the default parameters except –minindelfrac (set to 0.05).18 variants were annotated using annovar (http://www.openbioinformatics.org/annovar)19 and missense variants were further annotated using align-gvgd (http://agvgd.iarc.fr).20 nonsense, frameshift, canonical splice site variants (positions −2 and −1 upstream of an exon start and +1 and+2 downstream of an exon end) and single nucleotide […]

2017
PMCID: 5800345
PMID: 28993434
DOI: 10.1136/jmedgenet-2017-104947

[…] were considered deleterious, except for variants located at the c-terminal of brca1 and brca2 (amino acid position 1856–1863 and 3326–3385, respectively). all deleterious and non-c0 variants as per align-gvgd were validated by sanger sequencing., analyses were based on the variants identified through the analysis of the next generation sequencing data only. carriers of large genomic […]

Align-GVGD institution(s)
International Agency for Research on Cancer Lyon, France; Department of Bioinformatics and Computational Biology, George Mason University Manassas, VA, USA; Department of Clinical Oncology, Institute of Development Aging and Cancer, Tohoku University Sendai, Japan

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