Biosof SNPDBE nsSNP database of functional effects

Biosof Bioinformatics SNPdbe – nsSNP database of functional effects


 

[Contact us for a price]

Biosof LLC
SNPdbe
In stock

Biosof "SNPdbe" – nsSNP database of functional effects

Most single amino acid substitutions (SAASs) lack experimental annotation of their functional impact. SNPdbe is a database and a software interface that is designed to fill the annotation gap left by the high cost of experimental testing for functional significance of protein variants. It joins related bits of knowledge, currently distributed throughout various databases, into a consistent, easily accessible, and updatable resource. We currently cover over 155,000 protein sequences which come from more than 2,600 organisms. Overall we reference more than one million SAASs consisting of natural variants, SAASs from mutagenesis experiments and sequencing conflicts.

For more details, please refer to the statistics overview.

   
   
   
   
   
   

SNPdbe offers the following pieces of information (if available) on each SAAS:

  • Experimentally derived functional and structural impact
  • Predicted functional effect
  • Associated disease
  • Average heterozygosity
  • Experimental evidence of the nsSNP
  • Evolutionary conservation of wildtype and mutant amino acid
  • Link-outs to external databases

Biosof offers a convenient user interface to query SAASs on the following levels:

  • Protein and gene identifiers and keywords
  • Disease keywords
  • Protein sequence on different sequence identity thresholds
  • Variant identifier (dbSNP rs, SwissVar, PMD) or specific mutant like XposY and specified sequence

 

Specifications

SNPDBe Schema

SNPdbe statistics (updated 2012/03/05)

 

Total counts:

Organisms: 2985
Protein sequences: 159142
SAASs: 1691464

Top ten organisms:

Organism SAASs Sequences
Homo sapiens (human) 967879 (57%) 31979 (20%)
Mus musculus (house mouse) 210047 (12%) 23796 (15%)
Oryza sativa (rice) 188848 (11%) 17040 (11%)
Bos taurus (cattle) 64057 (4%) 8241 (5%)
Rattus norvegicus (Norway rat) 40245 (2%) 10326 (6%)
Canis lupus familiaris (dog) 22285 (1%) 11693 (7%)
Danio rerio (zebrafish) 16586 (1%) 6181 (4%)
Escherichia coli K-12 (None) 15604 (1%) 1339 (1%)
Gallus gallus (chicken) 13854 (1%) 5511 (3%)
Pan troglodytes (chimpanzee) 11811 (1%) 8799 (6%)

Predicted functional effect:

  Effect No effect No prediction
SNAP: 781543 (46%) 895093 (53%) 14828 (1%)
SIFT: 578864 (34%) 1029746 (61%) 82854 (5%)

Human variants:

Overall: 967879 (100%)
Observed functional effect: 23121 (2%)
Disease associations: 26842 (3%)
Observed functional effect and disease: 1629 (0%)

Contributions of underlying data sources:

SwissProt:

Overall SAASs: 220851 (100%)
Functional effect: 23121 (17%)
Disease associations: 26842 (12%)
SAAS type: VARIANT: 80006 (36%); MUTAGEN: 38245 (17%); CONFLICT: 102600 (46%)
SAASs with functional or
structural features :
47043 (21%)

PMD:

Overall SAASs: 87,439 (100%)
Functional effect: 72,738 (83%)
Structural effect: 7,933 (9%)
Disease associations: 6,768 (8%)




Underlying database builts

SwissProt: 2012_01
dbSNP:
  Norway rat (taxid 10116): b130
  dog (taxid 9615): b126
  Rhesus monkey (taxid 9544): b128
  rice (taxid 4530): b128
  gray short-tailed opossum (taxid 13616): b128
  cattle (taxid 9913): b131
  platypus (taxid 9258): b130
  hybrid cattle (taxid 30522): b128
  honey bee (taxid 7460): b128
  chimpanzee (taxid 9598): b127
  house mouse (taxid 10090): b131
  human (taxid 9606): b135
  chicken (taxid 9031): b128
  zebrafish (taxid 7955): b130
1000 Genomes: Release May 21 2011
PMD (unmaintained): March 2007


 

Database schema documentation for SNPdbe (schema.pdf, 91 Kb) [Download]

Application Note - SNPdbe: constructing an nsSNP functional impacts database (601.full.pdf_html, 6 Kb) [Download]

No posts found

None