t2prhd is a Perl script which generates simple diagrams that highlight relationships of sequence repeats detected by using a profile HMM in two sequences. Homology relations are identified on the basis of the phylogeny of repeats.

The approach is described in: Sipos, B., Somogyi, K., Pénzes, Zs., Andó, I. (2008) t2prhd: a tool to study the patterns of repeat evolution. - BMC Bioinformatics 9: 27 [doi:10.1186/1471-2105-9-27].

Manual page: Text PDF The manual page is embedded in the script in POD format, readily available by issuing "perldoc t2prhd". Due to resource limitations, the script is no longer accessible as an online tool.



The executable files must be installed in the path. If you use Linux simply install the required software using your favourite package manager.

Viewing the output

Example output

The output generated for Homo sapiens (TXH, gb|AAB47488.1) and Mus musculus (TXM, gb|AAB82015.1) Tenascin X amino acid sequences with the profile HMM of the Fibronectin type III domain (Pfam: PF00041): SVG PNG (rasterized SVG).

[TXH_vs_TXM output]

Command line used: t2prhd -p -w 2 -r 500x1500 -m fn3.hmm TXH.fas TXM.fas ;

Other example runs: download

Do not forget to use short sequence names (consult the manual page for the reason)!

The addition of new features is not planned, but bug reports are welcome to sbotond ( a t ) users.sourceforge.net.

SourceForge.net Logo Valid XHTML 1.0 Transitional SpamPoison