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  • Web report
  • Open Access

A novel approach to analyzing SNPs

Genome Biology20013:reports2006

https://doi.org/10.1186/gb-2001-3-1-reports2006

  • Received: 6 November 2001
  • Published:

Abstract

PicSNP is a browseable catalog of nonsynonymous single-nucleotide polymorphisms (nsSNPs - that is, base changes that alter the amino-acid sequence) in the human genome

Keywords

  • Gene Ontology
  • Public Database
  • Base Change
  • Ontology Category
  • SwissProt Database

Content

PicSNP is a browseable catalog of nonsynonymous single-nucleotide polymorphisms (nsSNPs - that is, base changes that alter the amino-acid sequence) in the human genome. Out of 1,190,295 SNPs extracted from public databases, 3,793 nsSNPs have been identified among 2,162 genes, and 2,826 nsSNPs (distributed among 1,506 genes) could be connected to 1,247 Gene Ontology categories of function, biological process or cellular components. Of the sites and domains annotated in the SwissProt database, 495 were found to include nsSNPs, including two nsSNPs in disulfide-binding sites and 38 in transmembrane regions. This website would, for example, be useful for searches for SNPs involved in common diseases.

Navigation

Reporter's comments

Timeliness

All the processes of constructing the catalog, from downloading the public database through creating the HTML pages will be fully automated by locally developed computer programs soon according to the website manager. This will ensure that data are fully coordinated with those of public data sources.

Best feature

The search output provides a brief summary of useful information on each gene identified as that contains an nsSNP, including information such as the biological processes in which the gene is involved (for example, behavior, cell-cell communication, cell growth).

Worst feature

The database is not very well known and it is not yet very extensive.

Related websites

The National Center for Biotechnology Information (NCBI) hosts the general database of single-nucleotide polymorphisms dbSNP. LocusLink and UniGene are useful for finding information about a particular gene or expressed sequence tag (EST).

Table of links

References

Copyright

© BioMed Central Ltd 2001

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