AS-IN Tool is a software package that predicts alternative splining rewiring effects. This tool should be used with Python 2.7. Anaconda distriburion is recommended.
AS-IN Tool depends on 2 software packages - EMBOSS and INTERPRO.
Direct download - ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-6.6.0.tar.gz
Could be downloaded from the EMBOSS website. In our package version 6.6.0 was used.
Direct download - ftp://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/5.27-66.0/interproscan-5.27-66.0-64-bit.tar.gz
Could be downloaded from the InterPro website. In our package version 5.27-66.0 was used.
We require two files to be accessible - pepstat from EMBOSS and insterproscan.sh from INTERPRO. If they are in the system path (i.e., accessible from the command line), no further actions required.
For each package that you cannot access from command line fill in corresponding line in 'config' file. E.g., to provide path for INTERPRO fill in empty space on the second line of the file: INTERPRO_PATH='~/Downloads/interproscan-5.27-66.0'
To actually make predictions you would need at least 2 files:
- Triplets consisting of the IDs of (Main isoform, Interacting partner, Alternatively spliced isoform) in tab separated format (.tsv)
- Fasta file(s) with protein sequences for the aforementioned protein IDs
To run our tool pleas use command in format
python [interactors_file.tsv] [output_file] [fasta_file_1, fasta_file_2, ...]
E.g., to run our test data you can use command
python asintool.py test/interactors.tsv test/results.txt test/diabetes_ensembl_protein.fa test/string_protein.fa
For questions, please email to the onarykov@wpi.edu