Difference between revisions of "Fabry:Sequence-based mutation analysis/Journal"
Rackersederj (talk | contribs) (→Scoring methods) |
Rackersederj (talk | contribs) (→Substitution matrices) |
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== Substitution matrices == |
== Substitution matrices == |
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| − | IN: [https://www.dropbox.com/s/qxaqmw62hkyfv3d/pickedSNPsNOINFO.txt pickedSNPsNOINFO.txt], BLOSUM62.csv, PAM250.csv<br> |
+ | IN: [https://www.dropbox.com/s/qxaqmw62hkyfv3d/pickedSNPsNOINFO.txt pickedSNPsNOINFO.txt], BLOSUM62.csv<ref>pynchon BLOSUM 62 [http://code.google.com/p/pynchon/source/browse/pynchon/bio/data/score/BLOSUM62 http://code.google.com/p/pynchon/source/browse/pynchon/bio/data/score/BLOSUM62]. June 12th. 2012</ref>, PAM250.csv<ref>pynchon PAM 250 [http://code.google.com/p/pynchon/source/browse/pynchon/bio/data/score/PAM250 http://code.google.com/p/pynchon/source/browse/pynchon/bio/data/score/PAM250]. June 12th. 2012</ref><br> |
OUT: SNP_substMatr.txt, SNP_substMatr.wiki |
OUT: SNP_substMatr.txt, SNP_substMatr.wiki |
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perl [http://dl.dropbox.com/u/13796643/fabry/seqbased_scripts/subst.pl.html subst.pl] |
perl [http://dl.dropbox.com/u/13796643/fabry/seqbased_scripts/subst.pl.html subst.pl] |
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Revision as of 12:01, 13 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
Location
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>pynchon BLOSUM 62 http://code.google.com/p/pynchon/source/browse/pynchon/bio/data/score/BLOSUM62. June 12th. 2012</ref>, PAM250.csv<ref>pynchon PAM 250 http://code.google.com/p/pynchon/source/browse/pynchon/bio/data/score/PAM250. June 12th. 2012</ref>
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
