https://github.com/dbogatov/asintool
Alternative Splicing INteraction prediction tool
Science Score: 13.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
○.zenodo.json file
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○DOI references
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○Academic publication links
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○Scientific vocabulary similarity
Low similarity (8.1%) to scientific vocabulary
Repository
Alternative Splicing INteraction prediction tool
Basic Info
- Host: GitHub
- Owner: dbogatov
- License: mit
- Language: Python
- Default Branch: master
- Size: 9.66 MB
Statistics
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
- Releases: 0
Metadata Files
README.md
AS-IN Tool
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.
INSTALLATION
AS-IN Tool depends on 2 software packages - EMBOSS and INTERPRO.
EMBOSS
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.
InterPro
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.
CONFIGURING
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'
RUNNING
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
SUPPORT
For questions, please email to the onarykov@wpi.edu
Owner
- Name: Dmytro Bogatov
- Login: dbogatov
- Kind: user
- Location: Boston, MA
- Website: https://dbogatov.org
- Twitter: dkbogatov
- Repositories: 43
- Profile: https://github.com/dbogatov