STIF API - Application Program Interface (API) to the Genome-scale prediction of plant stress responsive transcription factor binding sites:

API to the Stif Algorithm can be accessed from 'http://capservices.ncbs.res.in/stif/run_stif' using a script written in any language. We are providing a Python script as sample that can be downloaded here. A sample fasta file also available.


The script can be run as follows: run_stif_client.py

python run_stif_client.py input_fasta_file


The input should a well formated FASTA file. sample.fasta

>AT3G14990 | chr3:5046407-5047516
TCTTTTTTAAAAGGGTAGATGGTAGACCTCATTTGCTAATTTTGATCCACATAAGTCAA
TAACAAATAATTCGGCTCGCTTGCGAAGCTAATGCATGAGCCACGTGTTTTGCTTTATA
TTTGGCTTTCTGTATTGAGACATTCTTCTTCATCCTAATTGTGAATGGAATATGTTGGA
CCCAACGAAGCCATCAAACATGGTTAAAACACACAAACATGTGATTTAATCTAGTTTAA
TTTCGTCTATTACAATATAAGTGAATTTTGACACACATCCTTGGATTATATCTAAAACG
TTAAGTTTGTTAAAAACACTTTGGACCGGATAATGGGTATTGATCATTTATTGTTTGTT
GCATGTTGGGTTAGAAATTAGAGATCATAACAAAAATCATGATTTCAGGCTGTCCATTT
TGAAAAATGTGTGTGTTTGTGTTAATTTGAATACACCGATTCATCCAAAAACCATCTGA
ACAGTCTCTTAATTAGTTTACCGTGTATATATATCATATTTATGGGATCATATTTGGTT
AAGTTTAACTAGTAGTTTCAAATTTCGCGTTAATAGCTATTTGAAAGGGTAGGAGTACT
TTTTCGACCGGTTAACACTCCCATATAAAGCCCATAAATTATTGGAACGCTACAAAATT
AACAAAACATCTCTTCAGAAGTTCGTCCGGTTTACTCTACTACAAAGTACATGTATCAA
AAACGACAACACGTGCTTCCACAAAATTAAGAACCAGGACGTGATGTCGTTGTTGTAAT
ACTTTTTTCTCGCCAACTTCACGCCGTCTTAGTTTACCGAAACCAAAGTGGCTTTTTCT
GATTTTATCCAATACAATGACGTGGAAAGACTCAAAAGAAGCTTTCGCCACGTTCCACC
AATGAATGTTCGACACGTATCGTCGAGTTTCTTTTTCTTTATGCTTACGTCATCGCACA
CGTCTATCTTCTTTTGGTTAAAGTGATAAAAAGGAAAGTCGTAAATGGCTTCGTCACTG
AGTCTTTCCTACTATTTTAACCCCATTAGTGACACTCCTTTCTTCTCCACTACACTCCA
TTTCTCTTTCTTCTTGACTCGACCATCGTTTCTCTAATCTCCGCAACT

The output will a tab seperated file. tab_output.tsv
Gene TF_Name Z-Score Start End
AT3G14990 Nac_box_NAC 2.8479 -786 -781
AT3G14990 G_box_bHLH 3.4202 -283 -278
AT3G14990 G_box_bHLH 3.4202 -900 -895
AT3G14990 G_box2_bZIP 2.1745 -157 -152
AT3G14990 Myb_box5_MYB 2.8646 -222 -217
AT3G14990 W_box_WRKY 1.4313 75 80
AT3G14990 Myb_box3_MYB 2.1563 -946 -941
AT3G14990 Myb_box1_MYB 1.4031 -946 -941
AT3G14990 HSE1_HSF 0.8235 -112 -105