Difference between revisions of "Fabry:Sequence-based mutation analysis/Journal"
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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 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 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 http://en.wikipedia.org/wiki/Proteinogenic_amino_acid#Chemical_properties]. June 12th, 2012</ref>, [https://www.dropbox.com/s/qxaqmw62hkyfv3d/pickedSNPsNOINFO.txt pickedSNPsNOINFO.txt]<br> |
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 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 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 http://en.wikipedia.org/wiki/Proteinogenic_amino_acid#Chemical_properties]. June 12th, 2012</ref>, [https://www.dropbox.com/s/qxaqmw62hkyfv3d/pickedSNPsNOINFO.txt pickedSNPsNOINFO.txt]<br> |
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OUT: SNP_aaProps.txt, SNP_aaProps.wiki |
OUT: SNP_aaProps.txt, SNP_aaProps.wiki |
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| − | perl [ |
+ | perl [https://dl.dropbox.com/u/13796643/fabry/seqbased/scripts/read_AAProp.pl.html read_AAProp.pl] |
== Secondary Structure == |
== Secondary Structure == |
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IN: [https://www.dropbox.com/s/qxaqmw62hkyfv3d/pickedSNPsNOINFO.txt pickedSNPsNOINFO.txt], P06280.dssp.ss, P06280.reprof.ss, P06280.psipred.ss (from [[Fabry:Sequence-based_analyses#Alpha-galactosidase_A_.28P06280.29 |Task 3]])<br> |
IN: [https://www.dropbox.com/s/qxaqmw62hkyfv3d/pickedSNPsNOINFO.txt pickedSNPsNOINFO.txt], P06280.dssp.ss, P06280.reprof.ss, P06280.psipred.ss (from [[Fabry:Sequence-based_analyses#Alpha-galactosidase_A_.28P06280.29 |Task 3]])<br> |
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OUT: SNP_secStruc.txt, SNP_secStruc.wiki |
OUT: SNP_secStruc.txt, SNP_secStruc.wiki |
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| − | perl [ |
+ | perl [https://dl.dropbox.com/u/13796643/fabry/seqbased/scripts/compare_seq_struc.pl.html compare_seq_struc.pl] |
== Substitution matrices == |
== Substitution matrices == |
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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> |
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> |
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OUT: SNP_substMatr.txt, SNP_substMatr.wiki |
OUT: SNP_substMatr.txt, SNP_substMatr.wiki |
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| − | perl [ |
+ | perl [https://dl.dropbox.com/u/13796643/fabry/seqbased/scripts/subst.pl.html subst.pl] |
== PSSM == |
== PSSM == |
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IN: Prediction.txt<br> |
IN: Prediction.txt<br> |
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OUT: SNP_Sift.txt, SNP_Sift.wiki |
OUT: SNP_Sift.txt, SNP_Sift.wiki |
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| − | perl [ |
+ | perl [https://dl.dropbox.com/u/13796643/fabry/seqbased/scripts/readSift.pl.html readSift.pl] |
=== Polyphen2 === |
=== Polyphen2 === |
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IN: [https://www.dropbox.com/s/qxaqmw62hkyfv3d/pickedSNPsNOINFO.txt pickedSNPsNOINFO.txt]<br> |
IN: [https://www.dropbox.com/s/qxaqmw62hkyfv3d/pickedSNPsNOINFO.txt pickedSNPsNOINFO.txt]<br> |
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OUT: Polyphen.batch |
OUT: Polyphen.batch |
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| − | perl [ |
+ | perl [https://dl.dropbox.com/u/13796643/fabry/seqbased/scripts/prepBatchPolyphen2.pl.html prepBatchPolyphen2.pl] |
IN: pph2-full.txt<br> |
IN: pph2-full.txt<br> |
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OUT: SNP_pph2.txt, SNP_pph2.wiki |
OUT: SNP_pph2.txt, SNP_pph2.wiki |
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| − | perl [ |
+ | perl [https://dl.dropbox.com/u/13796643/fabry/seqbased/scripts/readPolyphen.pl.html readPolyphen.pl] |
=== SNAP === |
=== SNAP === |
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Revision as of 16:32, 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
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>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
