Difference between revisions of "Fabry:Sequence-based mutation analysis/Journal"
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== Substitution matrices == |
== Substitution matrices == |
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| − | IN: [https://dl.dropbox.com/u/13796643/fabry/seqbased/data/pickedSNPsNOINFO.txt pickedSNPsNOINFO.txt], |
+ | IN: [https://dl.dropbox.com/u/13796643/fabry/seqbased/data/pickedSNPsNOINFO.txt pickedSNPsNOINFO.txt], |
| + | [https://dl.dropbox.com/u/13796643/fabry/seqbased/data/BLOSUM62.csv BLOSUM62.csv]<ref>Koders BLOSUM 62 [http://www.koders.com/noncode/fidCE20DD761F1B6E8647B7EA1E8F4FCFF64C96F3B4.aspx]. June 12th. 2012</ref>, |
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| − | OUT: SNP_substMatr.txt, SNP_substMatr.wiki |
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| + | [https://dl.dropbox.com/u/13796643/fabry/seqbased/data/PAM250.csv PAM250.csv]<ref>Koders PAM250 [http://www.koders.com/noncode/fid383C7F1CDF7804C56F879E5725F36292EA24DEDE.aspx]. June 12th. 2012</ref>, |
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| + | [https://dl.dropbox.com/u/13796643/fabry/seqbased/data/PAM1.csv PAM1.csv] (thank you [[CD_task6_protocol#PAM1 | Canavan Disease Group]])<br> |
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| + | OUT: |
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| + | [https://dl.dropbox.com/u/13796643/fabry/seqbased/data/SNP_substMatr.txt SNP_substMatr.txt], |
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| + | [https://dl.dropbox.com/u/13796643/fabry/seqbased/data/SNP_substMatr.wiki SNP_substMatr.wiki] |
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perl [https://dl.dropbox.com/u/13796643/fabry/seqbased/scripts/subst.pl.html subst.pl] |
perl [https://dl.dropbox.com/u/13796643/fabry/seqbased/scripts/subst.pl.html subst.pl] |
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Revision as of 10:26, 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/>
