In Silico Functional Assessment of Sequence Variations: Predicting Phenotypic Functions of Novel Variations
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"In Silico Functional Assessment of ..." refers background in this paper
...The Swiss-Prot, dbSNP, and HapMap databases provide fundamental information on neutral polymorphisms....
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...The Swiss-Prot/TrEMBL databases and PSI-BLAST were used for sequence alignment....
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...Polymorphism and mutation databases Database Recent release date* Data type Features Website OMIM (Hamosh et al., 2005) Updated daily Deleterious mutations Full-text descriptions of published disease-causing variations http://www.ncbi.nlm.nih. gov/omim HGMD (Stenson et al., 2008) Sept 2008 Deleterious mutations Comprehensive collection of published disease-causing variations http://www.hgmd.cf.ac.uk LSDB in HGVS Nov 2008 Deleterious mutations Specialized collection of a particular gene or locus http://www.hgvs.org/dblist/ glsdb.html Swiss-Prot (Yip et al., 2004) Nov 2008 Deleterious mutations and neutral polymorphisms Well-summarized list of variations and corresponding proteins http://www.expasy.org/ cgi-bin/lists?humsavar.txt dbSNP (Sherry et al., 2001) Apr 2008 Neutral and (few) deleterious SNPs Broad collections of SNPs regardless of clinical associations (clinically associated SNPs linked to source sites) http://www.ncbi.nlm.nih. gov/projects/SNP dbGaP (Mailman et al., 2007) Nov 2008 Deleterious or pheno- type-affecting SNPs Collections of SNPs affecting clinical phenotypes or nonclinical traits http://www.ncbi.nlm.nih. gov/gap HapMap (Frazer et al., 2007) Oct 2008 Neutral SNPs and (very few) deleterious SNPs Collections of SNPs of 270 individuals randomly selected from African, Asian, and European populations http://www.hapmap.org *Accessed Nov 2008....
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...…LSDB in HGVS Nov 2008 Deleterious mutations Specialized collection of a particular gene or locus http://www.hgvs.org/dblist/ glsdb.html Swiss-Prot (Yip et al., 2004) Nov 2008 Deleterious mutations and neutral polymorphisms Well-summarized list of variations and corresponding…...
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...Random forest was trained with various features, such as structural information, sequence conservation, and SIFT prediction using a dataset from Swiss-Prot....
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"In Silico Functional Assessment of ..." refers background in this paper
...…advancements in sequencing technologies, several studies have reported a number of sequence variations in certain cancers (Sjoblom et al., 2006; Greenman et al., 2007; Campbell et al., 2008; Jones et al., 2008), in which mutational patterns have differed greatly between patients with the same…...
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3,721 citations
"In Silico Functional Assessment of ..." refers background in this paper
...…in sequencing technologies, several studies have reported a number of sequence variations in certain cancers (Sjoblom et al., 2006; Greenman et al., 2007; Campbell et al., 2008; Jones et al., 2008), in which mutational patterns have differed greatly between patients with the same disease....
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...Using recent advancements in sequencing technologies, several studies have reported a number of sequence variations in certain cancers (Sjoblom et al., 2006; Greenman et al., 2007; Campbell et al., 2008; Jones et al., 2008), in which mutational patterns have differed greatly between patients with the same disease....
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