How To Exon-Intron Map With Given Coordinates?

Question

[manish]

Hi,

I have transcript coordinate data and i need to plot intron-exon map from it.

In the table below T1, T2 ... are Transcirtps and E1, E2 ... are exons. Their corresponding coordinates range is given 0-1205 whic means starting from 0 to 1205.

                E1    E2    E3    E4    E5    E6 
            T1    0-1205    1206-1261    1262-1325    1326-1396    1397-1469    
            T2    0-1205    1206-1261    1262-1325    1326-1396    1397-1420    1421-1469
            T3    0-1205        1206-1269    1270-1340    1341-1364    1365-1413
            T4    0-1205        1206-1269    1270-1340    1341-1413

How can i plot it like image shown in Data visualisation -- exon/intron map? post.

Regards

Answer 1

[Vitis]

Gbrowse has a nice system to visualize this kind of structure. I'm sure some of the bio::graphics perl modules used by Gbrowse could be used as standalone script to make such graphs. http://www.bioperl.org/wiki/HOWTO:Graphics

Answer 2

[Alex Reynolds]

If you can convert your data matrix into GFF3-formatted elements, GenomeTools offers gt sketch that might help you out.