TargetPredict 0.1

Find the targets of a short RNA in the transcriptome using BLASTN and MIRANDA

Creation : 2015/03/08

Last update : 2015/03/25

Motivation and Principle

This program was develop to detect imperfect off-target effects of a small RNA in the human transcriptome.

GffFastaExtractor.py

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.

TargetPredict.py

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.

Dependencies

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+

Get and install TargetPredict

Clone the repository git clone https://github.com/a-slide/TargetPredict.git
Enter the src folder of the program folder
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

Usage

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')

Authors and Contact

Adrien Leger - 2015