Prosnp

From GersteinInfo

Revision as of 13:04, 28 July 2011 (view source) Public (Talk | contribs) (Created page with 'prosnp') ← Older edit		Latest revision as of 02:26, 7 August 2011 (view source) Public (Talk | contribs)
(12 intermediate revisions not shown)
Line 1:		Line 1:
-	prosnp	+	==Data from "Comparing selective pressure at protein-coding sites across broad evolutionary time-scales" by Khurana et al==
		+
		+	Omega (dN/dS) values for all coding sites in Gencodev3b computed from 12 whole-genome vertebrate alignments using PAML.
		+	[http://archive.gersteinlab.org/prosnp/all_omega omega_values_for_all_codons]
		+
		+	Omega values for sites identified as being under positive selection in humans relative to vertebrates (omega > 1 and probability (omega>1) > 0.5)
		+	[http://archive.gersteinlab.org/prosnp/omega_pos_sel Codons_under_positive_selection]
		+
		+	Allele frequencies of non-synonymous SNPs at sites that are identified as being under positive selection in humans relative to vertebrates and are polymorphic amongst humans
		+	in 1000 Genomes Pilot 1 data
		+	[http://archive.gersteinlab.org/prosnp/pos_sel_snps Pos_sel_SNP sites]
		+
		+
		+	Gap_scores for deletions from 1000 Genomes Pilot 1 data (1KG-DELs) computed from 28 whole-genome vertebrate alignments
		+	[http://archive.gersteinlab.org/prosnp/gap_score_1kg 1KG-gap_scores]
		+
		+	Gap_scores for disease-causing deletions from HGMD (HGMD-DELs) computed from 28 whole-genome vertebrate alignments
		+	[http://archive.gersteinlab.org/prosnp/gap_score_hgmd HGMD-gap_scores]
		+
		+	Structural conservation scores for non-synonymous SNPs from 1000 Genomes Pilot 1 data (1KG-SNPs)
		+	[http://archive.gersteinlab.org/prosnp/str_cons_1kg 1KG-str_cons_scores]
		+
		+	Structural conservation scores for disease-causing non-synonymous single nucleotide variants from HGMD (HGMD-SNVs)
		+	[http://archive.gersteinlab.org/prosnp/str_cons_hgmd HGMD-str_cons_scores]

---

Latest revision as of 02:26, 7 August 2011

Data from "Comparing selective pressure at protein-coding sites across broad evolutionary time-scales" by Khurana et al

 Omega (dN/dS) values for all coding sites in Gencodev3b computed from 12 whole-genome vertebrate alignments using PAML.
 omega_values_for_all_codons

 Omega values for sites identified as being under positive selection in humans relative to vertebrates (omega > 1 and probability (omega>1) > 0.5)
 Codons_under_positive_selection

 Allele frequencies of non-synonymous SNPs at sites that are identified as being under positive selection in humans relative to vertebrates and are polymorphic amongst humans 
 in 1000 Genomes Pilot 1 data
 Pos_sel_SNP sites 
 

 Gap_scores for deletions from 1000 Genomes Pilot 1 data (1KG-DELs) computed from 28 whole-genome vertebrate alignments
 1KG-gap_scores  

 Gap_scores for disease-causing deletions from HGMD (HGMD-DELs) computed from 28 whole-genome vertebrate alignments
 HGMD-gap_scores  

 Structural conservation scores for non-synonymous SNPs from 1000 Genomes Pilot 1 data (1KG-SNPs)
 1KG-str_cons_scores  

 Structural conservation scores for disease-causing non-synonymous single nucleotide variants from HGMD (HGMD-SNVs)
 HGMD-str_cons_scores