biofold/meta-snp repository overview

⁠Meta-SNP

⁠Meta-predictor of disease causing variants

https://snps.biofold.org/meta-snp⁠
For information and bugs contact:
emidio.capriotti (at) gmail.com

⁠Emidio Capriotti, 2013.

⁠Meta-SNP scripts are released under the Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) license.

The container includes the following packages and databases licensed by other researchers:

• PhD-SNP
• PANTHER 6.1 Library
• SNAP and dependencies
• SIFT
• blast2.2.26
• hmmer-2.3.2
• UniRef90 (Nov 2009)

⁠Example 1:

    Run predictions inside the docker image

    > python /home/bass/Meta-SNP/metasnp.py /home/bass/Meta-SNP/Test/fileseq.seq /home/bass/Meta-SNP/Test/filemuts.txt  -d /home/bass/Meta-SNP/Test/output/ -o /home/bass/Meta-SNP/Test/output/output.txt

⁠Example 2:

    Run the command 1 outside the docker image mounting the personal home directory inside the docker image:

    > docker run -v $HOME:/home/$USER  --rm -it  biofold/meta-snp:full python /home/bass/Meta-SNP/metasnp.py /home/bass/Meta-SNP/Test/fileseq.seq /home/bass/Meta-SNP/Test/filemuts.txt -o /home/$USER/test/output.txt -d /home/$USER/test/ -o /home/$USER/test/output.txt

⁠Please cite:

• Capriotti E, Altman RB, Bromberg Y (2013). Collective judgment predicts disease-associated single nucleotide variants. BMC Genomics. 14 Suppl 3:S2. PMID:23819846.
• Capriotti E, Calabrese R, Casadio R (2006). Predicting the insurgence of human genetic diseases associated to single point protein mutations with support vector machines and evolutionary information. Bioinformatics. 22(22):2729-2734. PMID:16895930.
• Thomas PD, Kejariwal A (2004) Coding single-nucleotide polymorphisms associated with complex vs. Mendelian disease: evolutionary evidence for differences in molecular effects. Proc Natl Acad Sci USA.101(43):15398-15403. PMID:15492219.
• Bromberg Y, Rost B (2007). SNAP: predict effect of non-synonymous polymorphisms on function. Nucleic Acids Res 35(11):3823-3835. PMID:17526529.
• Ng PC, Henikoff S (2003). SIFT: Predicting amino acid changes that affect protein function. Nucleic Acids Res. 31(13):3812-3814.. PMID:12824425.

⁠Disclaimer:

Maintainers have no responsibility for any damage resulting from the use of this tool.