Fabry:Sequence-based mutation analysis/Journal

Fabry Disease » Sequence-based mutation analysis » Journal

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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>, ip.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

OUT: SNP_aaProps.txt, SNP_aaProps.wiki

perl read_AAProp.pl

Secondary Structure

IN: pickedSNPsNOINFO.txt, P06280.dssp.ss, P06280.reprof.ss, P06280.psipred.ss (from Task 3)
OUT: SNP_secStruc.txt, SNP_secStruc.wiki

perl compare_seq_struc.pl

Substitution matrices

IN: pickedSNPsNOINFO.txt, BLOSUM62.csv<ref>Koders BLOSUM 62 [1]. June 12th. 2012</ref>, PAM250.csv<ref>Koders PAM250 [2]. June 12th. 2012</ref>, PAM1.csv (thank you Canavan Disease Group)
OUT: SNP_substMatr.txt, SNP_substMatr.wiki

perl subst.pl

PSSM

bash run_psi_blast.sh

Scoring methods

SIFT

IN: Prediction.txt
OUT: SNP_Sift.txt, SNP_Sift.wiki

 perl readSift.pl

Polyphen2

IN: pickedSNPsNOINFO.txt
OUT: Polyphen.batch

 perl prepBatchPolyphen2.pl

IN: pph2-full.txt
OUT: SNP_pph2.txt, SNP_pph2.wiki

 perl readPolyphen.pl

SNAP

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.

bash 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

IN: SNP_aaProps_final.wiki, SNP_secStruc.wiki, SNP_substMatr.wiki, SNP_Sift.wiki, SNP_pph2.wiki

OUT: overview.wiki, overview.txt

perl createOverviewTable.pl

References

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