Difference between revisions of "Fabry:Sequence-based mutation analysis/Journal"
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[[Fabry Disease]] » [[Fabry:Sequence-based_mutation_analysis|Sequence-based mutation analysis]] » Journal |
[[Fabry Disease]] » [[Fabry:Sequence-based_mutation_analysis|Sequence-based mutation analysis]] » Journal |
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<hr> |
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| + | [[Category: Fabry Disease 2012]] |
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| − | |||
| − | INSERT IMPORTANT AND INTELLIGENT STUFF RIGHT HERE |
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== Amino acid properties == |
== Amino acid properties == |
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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>, 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> |
OUT: SNP_aaProps.txt, SNP_aaProps.wiki |
OUT: SNP_aaProps.txt, SNP_aaProps.wiki |
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perl [http://dl.dropbox.com/u/13796643/fabry/seqbased_scripts/read_AAProp.pl.html read_AAProp.pl] |
perl [http://dl.dropbox.com/u/13796643/fabry/seqbased_scripts/read_AAProp.pl.html read_AAProp.pl] |
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== Location == |
== Location == |
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| − | IN: 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> |
OUT: SNP_secStruc.txt, SNP_secStruc.wiki |
OUT: SNP_secStruc.txt, SNP_secStruc.wiki |
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perl [http://dl.dropbox.com/u/13796643/fabry/seqbased_scripts/compare_seq_struc.pl.html compare_seq_struc.pl] |
perl [http://dl.dropbox.com/u/13796643/fabry/seqbased_scripts/compare_seq_struc.pl.html compare_seq_struc.pl] |
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== Substitution matrices == |
== Substitution matrices == |
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| − | IN: pickedSNPsNOINFO.txt, BLOSUM62.csv, PAM250.csv<br> |
+ | IN: [https://www.dropbox.com/s/qxaqmw62hkyfv3d/pickedSNPsNOINFO.txt pickedSNPsNOINFO.txt], BLOSUM62.csv, PAM250.csv<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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=== SIFT === |
=== SIFT === |
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=== Polyphen2 === |
=== Polyphen2 === |
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| − | IN: pickedSNPsNOINFO.txt<br> |
+ | IN: [https://www.dropbox.com/s/qxaqmw62hkyfv3d/pickedSNPsNOINFO.txt pickedSNPsNOINFO.txt]<br> |
OUT: Polyphen.batch |
OUT: Polyphen.batch |
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perl [http://dl.dropbox.com/u/13796643/fabry/seqbased_scripts/prepBatchPolyphen2.pl.html prepBatchPolyphen2.pl] |
perl [http://dl.dropbox.com/u/13796643/fabry/seqbased_scripts/prepBatchPolyphen2.pl.html prepBatchPolyphen2.pl] |
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=== SNAP === |
=== SNAP === |
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| − | |||
| − | |||
| − | [[Category: Fabry Disease 2012]] |
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Revision as of 09:05, 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, PAM250.csv
OUT: SNP_substMatr.txt, SNP_substMatr.wiki
perl subst.pl
PSSM
Multiple sequence alignment
Scoring methods
SIFT
Polyphen2
IN: pickedSNPsNOINFO.txt
OUT: Polyphen.batch
perl prepBatchPolyphen2.pl
