Control Panel: Existing web sites for querying genes and SNPs in human genome and my comments

Limitation for the databases below:

• Only SNPs mapped by NCBI can be found. 
• Except for SNPper, most can't analyze user's own SNPs. SNPper can map SNP to goldenpath now.

Latest original databases:  (http://www.ncbi.nlm.nih.gov/mapview/stats/BuildList.cgi?type=org#Homosapiens )

• Genome Assembly:  NCBI human build 36 (version 1) (Nov 2005)
• dbSNP: build 126 (Mar 02, 2006)
• Unigene: Build 188 (Dec 2005)

Ensembl  EnsMart Genome Browser (MartView):    Genomic position-based SNP or Gene query.

MartView Select the dataset for this query Focus:   Vega SNP Ensembl 37 Species:  Anopheles gambiae genes (AgamP3) (AgamP3)Apis mellifera genes (AMEL2.0) (AMEL2.0)Bos taurus genes (Btau_2.0) (Btau_2.0)Caenorhabditis elegans genes (CEL150) (CEL150)Canis familiaris genes (BROADD1) (BROADD1)Ciona intestinalis genes (JGI2) (JGI2)Drosophila melanogaster genes (BDGP4) (BDGP4)Danio rerio genes (ZFISH5) (ZFISH5)Fugu rubripes genes (FUGU4) (FUGU4)Gallus gallus genes (WASHUC1) (WASHUC1)Homo sapiens genes (NCBI35) (NCBI35)Monodelphis domestica genes (BROADO2) (BROADO2)Macaca mulatta genes (MMUL_0_1) (MMUL_0_1)Mus musculus genes (NCBIM34) (NCBIM34)Pan troglodytes genes (CHIMP1A) (CHIMP1A)Rattus norvegicus genes (RGSC3.4) (RGSC3.4)Saccharomyces cerevisiae genes (SGD1) (SGD1)Tetraodon nigroviridis genes (TETRAODON7) (TETRAODON7)Xenopus tropicalis genes (JGI4) (JGI4)

• Comprehensive data collection;
• A lot of options/settings to make;
• Multiple output formats, very friendly to further data processing;
• Gene or chromosomal region-based query;
• One chromosomal region each query;
• No extended SNP sequence (only 25 bp each end)

Current database:

• Goldenpath: hg17, (NCBI Build 35)
• dbSNP: Filtered from build 125
• Unigene: N/A (use Ensembl's transcripts)

<=back to top

NCBI MapView:   Genomic position-based SNP and Gene query. 

• "Data As Table View" provides HTML format tables- terrible format for data processing; 
• One chromosomal region each view/query;
• Max 5000 records download; 
• A lot of links, instead of immediately usable data; not suitable for large-scale data mining;
• No extended SNP sequence (as submitter provided for dbSNP);

  Good for:

  • Obtaining gene symbol list in a region;
  • Unigene-based EST/mRNA/gDNA alignments in small region - exon positions;
  • CpG island list;

  Not Good for:

  • comprehensive data collection and further data mining;
  • large-region analysis;
  • multiple region analysis;

Current database:

• Genome Assembly:  NCBI human build 35 (version 1)
• dbSNP: build 125
• Unigene: Build 188

<=back to top

UCSC Genome Browser:    Gene and SNP map query.

• One genomic region per query/view;
• "Tables" can produce a list of one type of data (for example, known gene, TSC SNPs, etc.) separately each time.
• SNP sequences have to be obtained separately. SNP data provide only 25 bp flanking sequence. 
• A universal sequence retrieval function is provided for FASTA format sequence regardless of SNP allele information.

Good for:

• find mapping positions for gDNA features, as genes, SNPs;
• graphic view of a single large region;

Not good for:

• multiple regions analysis;
• compiling of variety of data types;

Current database:

• Goldenpath: hg17, (NCBI Build 35)
• dbSNP: build ? (?)
• Unigene: Build ? (?)

<=back to top

SNPper

• Find genes by name, position or cytogenetic band.
• Find SNPs by name, position or cytogenetic band.
• Very good interface.
• Database delay can be long.
• New function support creating user's own private SNP database with mapping info.

Current database:

• Goldenpath: hg17 (NCBI Build 35)
• dbSNP: build 123

<=back to top

GenCards

    Provides comprehensive information of genes/proteins, especially expression data compiled from microarray data.

    Batch query using "OR". But detailed information can be viewed only individually.

Current version: Nov 9, 2005 (v2.33)

<=back to top

Authors: Chunyu Liu, Tu Nguyen

Updated: March 02, 2006