G-quadruplex identification and secondary structure stability prediction tool
G4Boost requires python3.
Prediction models was constructed using the sklearn module. Prebuilt regression and classification models are available through GitHub.
Locate regression and classification models (G4Boost_regressor.json and G4Boost_classifier.json) into the same directory with G4Boost.py
required python packages:
pandas==1.4.3
xgboost==1.4.2
Options:
--version show program's version number and exit
-h, --help show this help message and exit
-f FASTA_FILE, --fasta FASTA_FILE
Query sequences in fasta format
--classifier JSON_FILE
Classification model in .json format [optional]
--regressor JSON_FILE
Regression model in .json format [optional]
-N MAX_LOOP_LENGTH, --maxloop MAX_LOOP_LENGTH
The maximum number of bases allowed within a loop region [default=12]
-n MIN_LOOP_LENGTH, --minloop MIN_LOOP_LENGTH
The minimum number of bases allowed within a loop region [default=1]
-G MAX_G_BASES, --maxG MAX_G_BASES
The maximum number of consecutive guanine bases allowed within a G-stem [default=7]
-g MIN_G_BASES, --minG MIN_G_BASES
The minimum number of consecutive guanine bases allowed within a G-stem [default=1]
-l NUMBER_OF_LOOPS, --loops NUMBER_OF_LOOPS
The maximum number of fleaxible loops separating the G-stems [default=11]
--noreverse
Do not search the reverse complement of the input fasta.
-q, --quiet
Do not print progress report (i.e. sequence names as they are scanned).
Prepare an input file (FASTA):
head test_sequence.fa
>test_seq_1
GGGCAGAAGGGAGGGCTGGGG
Locate regression and classification models into the same directory with G4Boost.py
To run G4Boost:
python3 G4Boost.py -f test_sequence.fa
The outputs include two files
-
a gff file for the position of the putative G4s
-
a csv file for the secondary structure predcition scores
head test_sequence.fa.gff
test_seq_1 0 21 test_seq_1_0_21 21 + GGGCAGAAGGGAGGGCTGGGG
head test_sequence.fa.g4scores.csv
seq seq_length g4motif length loops G-quartet maxlbase minlbase G C GG CC g4_pred g4_prob mfe_pred
test_seq_1 21 GGGcagaaGGGaGGGctgGGG 21 3 3 5 1 66 9 42 0 1 0.99999976 -13.413148
To change parameters:
python3 G4Boost.py -f test_sequence.fa --maxloop 7 --minloop 1 --maxG 4 --minG 3 --loops 3 --noreverse --quiet