Format of Landmark Flat Files

Landmarks are genes that are found on either side of a pseudogene. We identify syntenic regions between two species by locating orthologous genes in the two species on either side of a pseudogene.

The landmark files give the gene anchors around each pseudogene which we used to identify syntenic regions between two species.


Data Description

In these files, the line starting with the ### indicates a human pseudogene defined by its chromosomal location and position in terms of start and end coordinates. The subsequent lines indicate the gene anchors between which the pseudogene is sandwiched and the start and end chromosomal positions of the gene are indicated. The exact field definitions are as follows:

  1. Name of the human gene
  2. Chromosome location of the gene
  3. Chromosome strand orientation
  4. Starting coordinate of the gene based on the chromosome
  5. End coordinate of the gene on the chromosome
  6. Name of the orthologous gene in the other species (chimp, mouse or rat)
  7. Chromosome location of the orthologous gene in the other species
  8. Chromosome strand orientation
  9. Starting coordinate of orthologous gene in the other species
  10. End coordinate of the ortholog on the chromosome in the other species