mirdita/hh-suite repository overview

⁠HH-suite3 for sensitive sequence searching

(C) Johannes Soeding, Markus Meier, Martin Steinegger, Milot, Mirdita, Michael Remmert, Andreas Hauser, Andreas Biegert

The HH-suite is an open-source software package for sensitive protein sequence searching based on the pairwise alignment of hidden Markov models (HMMs).

⁠Documentation

We provide an extensive user guide⁠ with many usage examples, frequently asked questions and guides to build your own databases.

⁠Installation

We recommend compiling HH-suite on the machine that should run the computations so that it can be optimized for the available CPU instruction sets.

⁠Compilation

To compile from source, you will need a recent C/C++ compiler (at least GCC 4.8 or Clang 3.6) and CMake⁠ 2.8.12 or later.

To download the source code and compile the HH-suite execute the following commands:

git clone https://github.com/soedinglab/hh-suite.git
cd hh-suite && mkdir build && cd build
cmake -DCMAKE_INSTALL_PREFIX=. ..
make -j 4 && make install
export PATH="$(pwd)/bin:$(pwd)/scripts:$PATH"

⁠Download Databases

Download current databases from our download server⁠. To build up multiple sequences alignments using HHblits, the Uniclust30 database is sufficient.

⁠Usage

For performing a single search iteration of HHblits, run HHblits with the following command:

hhblits -i <input-file> -o <result-file> -n 1 -d <database-basename>

For generating an alignment of homologous sequences:

hhblits -i <input-file> -o <result-file> -oa3m <result-alignment> -d <database-basename>

A detailed list of options for HHblits is available by running HHblits with the -h parameter.

⁠Reference

Steinegger M, Meier M, Mirdita M, Vöhringer H, Haunsberger S J, and Söding J (2019) HH-suite3 for fast remote homology detection and deep protein annotation, bioRxiv, 560029. doi: 10.1101/560029⁠

⁠Links

• Soeding lab⁠
• Databases for the HH-suite⁠