Find the targets of a short RNA in the transcriptome using BLASTN and MIRANDA
Creation : 2015/03/08
Last update : 2015/03/25
This program was develop to detect imperfect off-target effects of a small RNA in the human transcriptome.
Extract the sequences from a fasta file corresponding to features location indicated in a gff file. Features in the gff files can be restricted to a list of chromosomes and a list of types. Features can be extended in 5' and 3' and overlapping features can be merged together.
Search targets for a query fasta sequence (short RNA) in a subject fasta sequence using Blastn and Miranda algorithms. The ouput of the program is parsed and returned as csv tables sorted according to the alignment score.
The program was developed under Linux Mint 17.2 and was not tested with other OS. In addition to a python2.7 envronment the following dependencies are required for proper program execution:
GffFastaExtractor.py
- Python package: Biopython 1.65 +
TargetPredict.py
- NCBI Blast 2.2.28+
- Miranda v3.3a+
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Clone the repository
git clone https://github.com/a-slide/TargetPredict.git -
Enter the src folder of the program folder
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Make the main scripts executable
sudo chmod u+x TargetPredict.py GffFastaExtractor.py -
Finally, add or link TargetPredict.py and GffFastaExtractor.py to your PATH
GffFastaExtractor.py
Usage: GffFastaExtractor.py -f FASTA_file -g GFF_file [...]
Options:
--version show program's version number and exit
-h, --help show this help message and exit
-f FASTA, --fasta=FASTA Path to the fasta file contaning the complete genome (can be gzipped)
-g GFF, --gff=GFF Path to the gff file containing annotations of the genome file (can be gzipped)
-o OFFSET, --offset=OFFSET Bases to extract before and after the feature (default 0)
--fusion Fuse overlapping features in a meta-feature (default False)
--output_gff Output the gff file corresponding to the extracted features sequences (default False)
--features=FEATURES Restrict extraction to a list of features. The list must be SPACE separated and quoted (default exon)
--chromosomes=CHROMOSOMES Restrict extraction to a list of chromosomes. The list must be SPACE separated and quoted (default all)
TargetPredict.py
Usage: TargetPredict.py -s SUBJECT -q QUERY [...]
Options:
--version show program's version number and exit
-h, --help show this help message and exit
-s SUBJECT, --subject=SUBJECT Path to the subject in fasta
-q QUERY, --query=QUERY Path to the query in fasta
--blastn_opt=BLASTN_OPT Options to run blastn (default='-task blastn-short -evalue 100000000 -word_size 5 -max_target_seqs 10000')
--miranda_opt=MIRANDA_OPT Options to run miranda (default='-sc 160')
Adrien Leger - 2015