QuanTest2 using Q score and TC score

modified by wym6912 (wym6912@outlook.com)

Using this repository by testing protein sequences provided by QuanTest2.

How to clone

Please clone this repository use the following command:

git clone https://github.com/malabz/QuanTest2 --recurse-submodules

How to test

Before testing, please check the varibles in script: program_name, cmd, prog_alias.

Then run the following command:

bash run.[program].sh # change the [program] to your program name

Result file is [program].txt.

Test_hasunknown folder

We checked all input sequences, found one sequence has unknown character U. We put this file into Test_hasunknown folder.

If you want to test the file into standard test, please run the following command:

cp Test_hasunknown/AhpC-TSA.vie Test/

References

QuanTest2: Sievers, F. & Higgins, D. G. Fabian Sievers, Desmond G Higgins, QuanTest2: benchmarking multiple sequence alignments using secondary structure prediction, Bioinformatics, Volume 36, Issue 1, January 2020, Pages 90–95, https://doi.org/10.1093/bioinformatics/btz552

PREFAB Q score: Robert C. Edgar, MUSCLE: multiple sequence alignment with high accuracy and high throughput, Nucleic Acids Research, Volume 32, Issue 5, 1 March 2004, Pages 1792–1797, https://doi.org/10.1093/nar/gkh340

SP and TC scores: J D Thompson and others, BAliBASE: a benchmark alignment database for the evaluation of multiple alignment programs., Bioinformatics, Volume 15, Issue 1, January 1999, Pages 87–88, https://doi.org/10.1093/bioinformatics/15.1.87