Alamut Visual protocols

View Alamut Visual computational protocol

Alamut Visual statistics

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Popular tool citations

chevron_left Variant effect prediction Variant visualization Splicing defect prediction chevron_right
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Associated diseases

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Alamut Visual specifications

Information


Unique identifier OMICS_05998
Name Alamut Visual
Software type Toolkit/Suite
Interface Command line interface
Restrictions to use License purchase required
Operating system Unix/Linux
License Commercial
Computer skills Advanced
Stability Stable
Maintained Yes

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Alamut Visual in pipelines

 (2)
2017
PMCID: 5748699
PMID: 29232904
DOI: 10.3390/genes8120381

[…] variants (134), were omitted in the analysis if they were not predicted to have an effect on a splice site. integrative genomics viewer v. 2.3.14 was used to visualize the bam data [], and alamut visual software 2.6 (interactive biosoftware, rouen, france) showed nucleotide and amino acid conservation scores., we report a distinct phenotype, which is hypothetically caused […]

2016
PMCID: 5392598
PMID: 27490115
DOI: 10.1038/gim.2016.118

[…] workbench v6.4 (qiagen), followed by postmapping duplicate-read removal, coverage analysis, and quality-based variant calling. more thorough variant annotation was executed with alamut-ht v1.1.5 and alamut visual v2.7 software (interactive biosoftware). for case 1, because we had access to parental dna, a trio-sequencing strategy was used. variant filtering was performed with the ingenuity […]


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Alamut Visual in publications

 (64)
PMCID: 5951831
PMID: 29760383
DOI: 10.1038/s41467-018-04322-5

[…] downloaded through the gdc portal. expression data of the tumors from uvm_1 and gbm_4 was explored through the cbioportal. effect of splice mutations was predicted on the major transcript with the alamut visual software (interactive software, rouen, france), which contains the algorithms splicesitefinder, maxentscan, nnsplice, genesplicer, human splicing finder, ese-finder, and rescue-ese. […]

PMCID: 5924558
PMID: 29673180
DOI: 10.3390/genes9040216

[…] bioinformatics tools. a detailed explanation on the background of scores for each algorithm included in the alamut splicing module can be found at http://www.interactive-biosoftware.com/doc/alamut-visual/2.6/splicing.html., the differences among age-groups and frameshifting/in-frame groups were evaluated for each parameter under study with fisher’s exact test. the chi-square trend test […]

PMCID: 5813712
PMID: 29472987
DOI: 10.1530/EDM-17-0139

[…] show avpr2 variants. variants with a population frequency greater than 1 in 50 were automatically deemed as insignificant., variant interpretation of the remaining variants was carried out using the alamut visual software. all variants of class 4 or above, according to the current acmg guidelines, were then confirmed by sanger sequencing (). the recurrent mutation c.409c > t, p.(arg137 cys) […]

PMCID: 5796507
PMID: 29390993
DOI: 10.1186/s12920-018-0320-7

[…] from the general population were considered to have moderate evidence as pathogenic. second, literature and database searches for previous reports and functional studies were performed using the alamut visual 2.6 software (interactive biosoftware, france) and hgmd professional database. when all in silico analyses showed consistent predictions, the results were regarded as evidence of benign […]

PMCID: 5792649
PMID: 29386597
DOI: 10.1038/s41598-018-20281-9

[…] each new molecular event was estimated with in silico prediction of protein function tools: polyphen (genetics.bwh.harvard.edu/pph), sift (sift.jcvi.org), mutationtaster (mutationtaster.org) using alamut visual version 2.7.1., the cdnas encoding human ldlr and human pcsk9 and its mutants were cloned in pires2-egfp (clontech labs), a bicistronic plasmid allowing the independent expression […]


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