Difference between revisions of "Fabry:Sequence-based mutation analysis/Journal"
Rackersederj (talk | contribs) (→SIFT) |
Rackersederj (talk | contribs) (→Polyphen2) |
||
| Line 41: | Line 41: | ||
=== Polyphen2 === |
=== Polyphen2 === |
||
| − | IN: [https:// |
+ | IN: [https://dl.dropbox.com/u/13796643/fabry/seqbased/data/pickedSNPsNOINFO.txt pickedSNPsNOINFO.txt]<br> |
| − | OUT: Polyphen.batch |
+ | OUT: [https://dl.dropbox.com/u/13796643/fabry/seqbased/data/Polyphen.batch Polyphen.batch] |
perl [https://dl.dropbox.com/u/13796643/fabry/seqbased/scripts/prepBatchPolyphen2.pl.html prepBatchPolyphen2.pl] |
perl [https://dl.dropbox.com/u/13796643/fabry/seqbased/scripts/prepBatchPolyphen2.pl.html prepBatchPolyphen2.pl] |
||
| − | IN: pph2-full.txt<br> |
+ | IN: [https://dl.dropbox.com/u/13796643/fabry/seqbased/data/pph2-full.txt pph2-full.txt]<br> |
| + | OUT: [https://dl.dropbox.com/u/13796643/fabry/seqbased/data/SNP_pph2.txt SNP_pph2.txt], [https://dl.dropbox.com/u/13796643/fabry/seqbased/data/SNP_pph2.wiki SNP_pph2.wiki] |
||
| − | OUT: SNP_pph2.txt, SNP_pph2.wiki |
||
perl [https://dl.dropbox.com/u/13796643/fabry/seqbased/scripts/readPolyphen.pl.html readPolyphen.pl] |
perl [https://dl.dropbox.com/u/13796643/fabry/seqbased/scripts/readPolyphen.pl.html readPolyphen.pl] |
||
Revision as of 10:28, 18 June 2012
Fabry Disease » Sequence-based mutation analysis » Journal
Contents
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
Multiple sequence alignment
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
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
<references/>
