Predicting the functional, molecular, and phenotypic consequences of amino acid substitutions using hidden Markov models.
Citations
4,658 citations
Cites methods from "Predicting the functional, molecula..."
...GWAVA [51], CADD [52], and FATHMM-MKL [53] plugins are also available, which integrate genomic and epigenomic factors to grade and prioritize non-coding variants....
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...Other pathogenicity predictor scores such as Condel [42], FATHMM [43], and MutationTaster [44] are available for human data via VEP plugins (Table 4)....
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1,623 citations
Cites background or methods from "Predicting the functional, molecula..."
...…designed to distinguish between driver and passenger somatic mutations (CHASM [Wong et al., 2011], CanDrA [Carter et al., 2013], fathmm [Shihab et al., 2013] and transFIC [Gonzalez-Perez et al., 2012]) and four tools that leverage information from protein structures (HotSpot3D [Niu et…...
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...…Ng and Henikoff, 2002 http://sift.jcvi.org PolyPhen2 Adzhubei et al., 2013 http://genetics.bwh.harvard.edu/pph2/ fathmm Shihab et al., 2013 http://fathmm.biocompute.org.uk transFIC Gonzalez-Perez et al., 2012 http://bbglab.irbbarcelona.org/transfic/home CTAT-score This…...
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...…version was run under default parameters using the ‘‘general’’ cancer type database. fathmm Functional Analysis Through Hidden Markov Models (fathmm) (Shihab et al., 2013) uses Hidden Markov modeling to represent the protein domain shared across human proteins and to estimate the functional…...
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...…[Ng and Henikoff, 2002], PolyPhen2 [Adzhubei et al., 2013], MutationAssessor [Reva et al., 2011], transFIC [Gonzalez-Perez et al., 2012], fathmm [Shihab et al., 2013], CHASM [Carter et al., 2009], CanDrA [Mao et al., 2013] and VEST [Carter et al., 2013]), 4 structure-based (HotSpot3D [Niu et…...
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1,295 citations
1,204 citations
Cites methods from "Predicting the functional, molecula..."
...…also been used by a number of different groups to aid the development of post-NGS variant interpretation algorithms including MutPred (Li et al. 2009), PROVEAN (Choi et al. 2012), CAROL (Lopes et al. 2012), CRAVAT (Douville et al. 2013), NEST (Carter et al. 2013) and FATHMM (Shihab et al. 2013)....
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...2013) and FATHMM (Shihab et al. 2013)....
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...HGMD has also been used by a number of different groups to aid the development of post-NGS variant interpretation algorithms including MutPred (Li et al. 2009), PROVEAN (Choi et al. 2012), CAROL (Lopes et al. 2012), CRAVAT (Douville et al. 2013), NEST (Carter et al. 2013) and FATHMM (Shihab et al. 2013)....
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1,053 citations
Additional excerpts
...HGMD has also been used by a number of different groups to aid the development of a wide variety of post-NGS variant interpretation and exome prioritisation algorithms including MutPred (Li et al. 2009), MutPred Splice (Mort et al. 2014), PROVEAN (Choi et al. 2012), CAROL (Lopes et al. 2012), regSNPs (Teng et al. 2012), CRAVAT (Douville et al. 2013), NEST (Carter et al. 2013), FATHMM (Shihab et al. 2013), FATHMM-MKL (Shihab et al. 2015), PinPor (Zhang et al. 2014), MutationTaster2 (Schwarz et al. 2014), Phen-Gen (Javed et al. 2014), VEST-indel (Douville et al. 2016), Gene Damage Index (Itan et al. 2015), DDIGin (Folkman et al. 2015), RSVP (Peterson et al. 2016), ExonImpact (Li et al. 2017), IntSplice (Shibata et al. 2016), snvForest (Wu et al. 2015), IMHOTEP (Knecht et al. 2017) and M-CAP (Jagadeesh et al. 2016)....
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...2013), FATHMM (Shihab et al. 2013), FATHMM-MKL (Shihab et al....
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...…PROVEAN (Choi et al. 2012), CAROL (Lopes et al. 2012), regSNPs (Teng et al. 2012), CRAVAT (Douville et al. 2013), NEST (Carter et al. 2013), FATHMM (Shihab et al. 2013), FATHMM-MKL (Shihab et al. 2015), PinPor (Zhang et al. 2014), MutationTaster2 (Schwarz et al. 2014), Phen-Gen (Javed et al.…...
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References
88,255 citations
"Predicting the functional, molecula..." refers background or methods in this paper
...Traditionally, the BLAST range of pairwise alignment [Altschul et al., 1990] and sequence profile algorithms [Altschul et al....
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...Traditionally, the BLAST range of pairwise alignment [Altschul et al., 1990] and sequence profile algorithms [Altschul et al., 1997] have been used to search large sequence databases for homologous proteins falling within a predefined similarity threshold....
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70,111 citations
"Predicting the functional, molecula..." refers methods in this paper
...Traditionally, the BLAST range of pairwise alignment [Altschul et al., 1990] and sequence profile algorithms [Altschul et al., 1997] have been used to search large sequence databases for homologous proteins falling within a predefined similarity threshold....
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..., 1990] and sequence profile algorithms [Altschul et al., 1997] have been used to search large sequence databases for homologous proteins falling within a predefined similarity threshold....
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35,225 citations
"Predicting the functional, molecula..." refers background in this paper
...For example, the molecular consequences of AASs are statistically inferred by mapping SUPERFAMILY [Gough et al., 2001] HMMs onto the Gene Ontology [Ashburner et al., 2000]....
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14,075 citations