HMM Profile-Profile alignment
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2.0 years ago

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

HMM GPCRs profile Alignment • 677 views
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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.

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2.0 years ago
biofalconch ★ 1.1k

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

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

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Hey, no they used HHblits to compare their results with

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