suzannejin/mod_quantest2 repository overview

⁠Modified QuanTest2

A containerized version of QuanTest2. NOTE: the quantest2.py script is modified to be able to use the standalone version of PSIPRED to predict the secondary structures.

This repository is created to store the Dockerfile and the modified scripts.

The original SOURCES are listed below in the REFERENCE section.

⁠Docker | Singularity

The docker image is accessible from suzannejin/mod_quantest2

You can also use it with singularity:

singularity pull docker://suzannejin/mod_quantest2:latest

In order to run the helper script get_refANDinformative_seqs.py, you should install T-coffee first. You can find its docker image in suzannejin/tcoffee or use it with singularity:

singularity pull docker://suzannejin/tcoffee:latest

and save it as 't_coffee' in a directory in your $PATH.

⁠Usage

quantest2 <alignment file> <ss file>

The alignment file should be in FASTA format.

The ss file should include the chosen 3 reference sequences per family. You can retrieve the most informative reference sequences by doing: t_coffee -other_pg seq_reformat -in -action +trim _aln_n3 -output fasta_seq

You can also use the get_refANDinformative_seqs.py script to retrieve N informative sequences from the alignment.

⁠Reference

⁠Main

QuanTest2:

Sievers, F. & Higgins, D. G. QuanTest2: benchmarking multiple sequence alignments using secondary structure prediction. Bioinformatics (2019). doi:10.1093/bioinformatics/btz552

⁠Dependency

DeepMSA:

Zhang, C., Zheng, W., Mortuza, S. M., Li, Y. & Zhang, Y. DeepMSA: constructing deep multiple sequence alignment to improve contact prediction and fold-recognition for distant-homology proteins. Bioinformatics (2019). doi:10.1093/bioinformatics/btz863

PSIPRED:

Jones, D. T. Protein secondary structure prediction based on position-specific scoring matrices 1 1Edited by G. Von Heijne. J. Mol. Biol. 292, 195–202 (1999).

T-coffee:

Notredame, C., Higgins, D. G. & Heringa, J. T-coffee: a novel method for fast and accurate multiple sequence alignment 1 1Edited by J. Thornton. J. Mol. Biol. 302, 205–217 (2000).

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