Mutalyzer

[…] database (hgmd) (http://www.hgmd.org/). the effects of these variants were evaluated with several types of predictive software, including (1) mutationtaster (http://www.mutationtaster.org/); (2) mutalyzer (https://mutalyzer.nl/); (3) spliceport (http://spliceport.cbcb.umd.edu), (4) alternative splice site predictor (assp) (http://wangcomputing.com/assp/index.html), and (5) human splicing […]

[…] seattleseq annotation: http://snp.gs.washington.edu/seattleseqannotation131/;, 1000 genomes: http://www.1000genomes.org/;, alamut: http://www.interactive-biosoftware.com/;, mutalyzer 2.0.beta-21: https://mutalyzer.nl/;, ncbi: http://www.ncbi.nlm.nih.gov/, genecards: http://www.genecards.org/, ensemble: http://www.ensembl.org/homo_sapiens/gene/, fshd genotyping […]

[…] using gatk [, ] and to check the presence of each variant in external databases (exac, 1000genome or clinvar) [–]. predictive values from selected prediction algorithms (for example sift [], mutation analyzer [], mutationtaster [], lrt [], polyphen-2 [], phylop [], gerp [], cadd [] or spidex (https://www.deepgenomics.com/spidex) were added to the annotated alternative variants., […]

[…] (cpm)., identification of translation initiation sites (tis) in ht treated samples was performed by a previously published bioinformatics peak calling analysis []. orf coordinates were assigned with mutalyzer []. in this analysis, peaks were defined as having >40% of all coverage in the first position and a minimum total coverage of 20. candidate peaks were considered […]

[…] to detect mutations in the coding sequence and exon/intron junctions of btk. the nomenclature for mutations in btk is according to guidelines by the human genome variation society as determined by mutalyzer 2.0.26-name checker (nm_000061.2)., table presents clinical findings and laboratorial data of the 20 patients and lists btk mutations identified in 17 participants. the mean age […]

[…] be described using the nomenclature devised by the hgvs nomenclature (http://varnomen.hgvs.org/) []. several software programs are available to ensure adherence to standardized nomenclature (e.g., mutalyzer; https://www.mutalyzer.nl/). variants should be described at both cdna and protein level, and the reference sequence number and version including the transcript and protein variant […]

[…] all pathogenic mutations were tested twice in two independent experiments. the nomenclature of the variants was based on the armc5 ncbi reference sequence nm_001105247.1 and was verified using the mutalyzer program (http://www.lovd.nl/mutalyzer/)., pbmah family-1 had 14 members including 9 who participated in the clinical data collection and gene sequencing (; ). the proband (ii-5 in family-1 […]