Fabry:Sequence-based mutation analysis/Journal
Amino acid properties
IN: aa_properties.txt<ref>Wikipedia, Amino Acid (June 11th, 2012), http://en.wikipedia.org/wiki/Amino_acid#Table_of_standard_amino_acid_abbreviations_and_properties. June 11th, 2012</ref>, resMass.txt<ref>ExPASy. The amino acid masses http://education.expasy.org/student_projects/isotopident/htdocs/aa-list.html. June 12th, 2012</ref>, pI.txt<ref>Wikipedia, Proteinogenic amino acid (May 20th, 2012) http://en.wikipedia.org/wiki/Proteinogenic_amino_acid#Chemical_properties. June 12th, 2012</ref>, pickedSNPsNOINFO.txt
BLOSUM62.csv<ref>Koders BLOSUM 62 . June 12th. 2012</ref>,
PAM250.csv<ref>Koders PAM250 . June 12th. 2012</ref>,
PAM1.csv (thank you Canavan Disease Group)
OUT: SNP_substMatr.txt, SNP_substMatr.wiki
Multiple sequence alignment
In order to gain predictions for every (non-silent) mutation at the positions of the selected SNPs, a new mutation file had to be generated. Since we are only interested in ten positions, SNAPs all keyword, was not an option. The mutations file was generated by the script snap_generate_mutations.sh.
We used the following command to obtain the SNAP2 predictions (see run_snap2.sh).
snap2 --tolerate -i P06280.fasta -m snap_mutations.txt -o P06280_snap2_result.txt |& tee snap2.log
Since snap2 exited with an error without the tolerate option, we had to add it to the command.
--tolerate Tolerate failures from external programs. Failures will trigger snap2 to switch into fallback mode (predictions will have lower accuracy)
Results and Conclusion