HMM Profile-Profile alignment

Question

[charlotte.crauwels]

Hey everyone,

I'm trying to reproduce the alignment method used in this paper https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4814114/pdf/pcbi.1004805.pdf (Structure-Based Sequence Alignment of the Transmembrane Domains of All Human GPCRs: Phylogenetic, Structural and Functional Implications). They create HMM profiles and then they align them.

Which software should I use for HMM profile-profile alignment? I cannot find any recent state of the art information about this.

Thank you in advance.

Best, Charlotte

[Joe]

You should be able to do profile-profile alignment with hmmer and likely hhsuite. I believe some multiple alignment tools like CLUSTAL can also do this but its been a while since I've tried so don't quote me on that.

Answer 1

[biofalconch]

The authors of the paper you provided mention they did the HMM-HMM alignment using HHblits.

https://github.com/soedinglab/hh-suite

[charlotte.crauwels]

Hey, no they used HHblits to compare their results with