I am looking for a project or tool that allows programmatic pairwise alignments of proteins but that takes care with transmembrane regions of proteins. TM regions are traditionally too information poor for many tools to align accurately (Wong et al, 2010).
- TM-aligner doesn't appear to have a program to download, and is only available via webserver. On the otherhand,
- PRALINE has some optimisation for TM regions, however was released in 2008 and since then there has been a boom in TM knowledge from structures so does not benefit from that.Currently I am using PSI-BLAST. However,
- PSI-Blast uses SEG to mask low complexity regions. This will most likely mean that TMHs are masked making the alignment of those regions fairly unreliable.
Primarily I am interesting in sequence alignments. But if anyone knows of a TM structural alignment, that could be good to know.
I think generally that counting idea works for an ideal helix, but a vast majority of TMHs break convention. I wouldn't expect to see a pattern based aligner that was that general. I'd be interested if anyone knows of a tool that juggles that though!
If I understand correctly, Matteo was saying that TMHs follow a simple patter (HHP/H,HHP/H...~7 times). This is not the case. There are too many examples of TMHs that do not match this pattern to assume this pattern would accurately align TMHs. As @MichaelG. suggests, the number of TMP structures has not caught up to their soluble counterparts in the database. I've updated the question to explain why PSI-Blast might not be the best option.