t2prhd

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.

Download

• Release 2.0
• Release 1.7.1
• View the Git repository

Requirements

• the BioPerl modules (version 1.4.0 or higher) - documentation
• the XML::Writer module - documentation
• the HMMER package version 2.3.2 or higher (hmmsearch and hmmalign) - user's guide
• CLUSTAL W: unix windows (tested with version 1.83) or PhyML (tested with version 2.4.4)

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

• The generated SVG file can be viewed by Firefox 1.5 or higher and can be rasterized (and also viewed) using the Batik toolkit or any other image editor capable to handle the SVG format. For rasterization you can also use this on-line converter.

• Requirements for processing the (optionally) generated LaTeX output:

  • LaTeX (pdflatex) or MiKTeX (windows)
  • LaTeX packages: TikZ xcolor fancyhdr preprint/fullpage

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).

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.

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