NCBI Map viewer

Finding a region by map position

Start at the NCBI human genome homepage, and choose one of the chromosomes from the image on right. We will focus on chromosome 4. Clicking on the chromosome image will take you to the map view for that chromosome:

The default map view shows (from left):

• In the blue panel an overview of the chromosome that you are looking at. The red lines show the region of the chromosome, and we will see how these alter as you zoom in and out.
• The first, banded, bar on the main image is the whole chromosome itself.
• UniGene_Hs. The grey histogram is the density of ESTs and mRNAs aligned to the sequence
• Genes_seq. Genes that have been annotated on the human genome. Genes shown on the left of the grey line are transcribed in the - orientation (from bottom up), and those on the right in the + orientation (from top down). The genes are also color coded:
  • Blue: Confirmed gene, alignment of mRNA and/or ESTs, to the genomic sequence
  • Light Green: EST only
  • Dark Brown: Predicted+EST - model predicted by GenomeScan and EST evidence
  • Light Brown: Predicted only - model predicted by GenomeScan
  • Orange: Conflict - there is some discrepancy between the mRNA sequence and the gene model
• symbol
• orient
• links
  • sv: sequence viewer
  • ev: evidence viewer
  • seq: sequence download
  • mm: model maker
• evidence
  • C:Confirmed gene, alignment of mRNA and/or ESTs, to the genomic sequence
  • E: EST only
  • PE: Predicted+EST - model predicted by GenomeScan and EST evidence
  • P: Predicted only - model predicted by GenomeScan
  • ?: Conflict - there is some discrepancy between the mRNA sequence and the gene model
  • I: Interim ID. Gene is not unambiguously placed
• cyto: cytogenetic position
• full name: name of the gene of locus.

Clicking on the will allow you to add more maps to this view. Many different maps are available, and the types of map depend on which organism you are working with. For example, this is the list of human maps available.

Each of the maps allows you to recenter, or zoom in or out. Some of the maps (e.g. the genes_seq amp) allows you to display different regions of the genome sequence

Finding a region by homology search

Here is some sequence

You can BLAST this sequence against the human genome here

When you get the BLAST result back, you get the standard blast view, but there is also a link that will take you to the genome view. Try it!

Here are the links for this result: NT_030642 and NT_004576. Note these links will expire around 5/16/02-5/17/02.

Synteny Maps

The links to the NCBI synteny maps are here

There are currently five maps available:

• NCBI vs. MGD: Uses the current NCBI assembly and the MGD genetic map.
• UCSC vs. MGD: Uses the current UCSC assembly and the MGD genetic map.
• NCBI vs. EST: Uses the current NCBI assembly and the Whitehead/MRC RH map.
• UCSC vs. EST: Uses the current genome UCSC assembly and the Whitehead/MRC RH map.
• Nature Genetics Paper: This uses the UCSC assembly based on the October 7th data freeze and the Whitehead/MRC RH Map as represented by (Hudson et al, 2001)

All maps work the same way. Choose the chromosome from the pull-down menu

And then click Go!

You will see a list of genes, and their homologs in the other genome. The chromosomes are color coded so that you can see regions of homology