Table 1 Description of data file types used by OmniMap and their use

posn

Any feature with a position and size on a chromosome or scaffold. For example, genes, primer sequences, markers, homologous regions. Needs chromosome ID, start and end nucleotide positions. The first #-line of the data determines what colour is used to display this region.

blast

Any sequence region identified in a blast search. Needs chromosome ID, start and end nucleotide positions and E-value. All data with E-values less than the E-value cut-off on the 2^nd #-line of the data are displayed.

expr

This allows different items in the same data file to be displayed in different colours. For example, with microarray expression data all up-regulated genes could be in red and all down-regulated genes in blue. The colour is determined by the last field on each data line.

freq

This is used to display frequency data. For example, recombination frequency between genetic markers or %GC across a chromosome in a gradient of colours. The value of the last field on a data line is used to determine which of 20 user-defined colours are displayed.

graph

This is used to draw a graph or histogram along a chromosome, for example SNP density. The value of the last field on a data line (e.g. number of SNPs/50,000 nt) is used to determine the y-value.