Difference between revisions of "Fabry:Sequence-based mutation analysis/Journal"

From Bioinformatikpedia
(→‎Amino acid properties)
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== Amino acid properties ==
  
== Amino acid properties ==
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IN:
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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://dl.dropbox.com/u/13796643/fabry/seqbased/data/pickedSNPsNOINFO.txt pickedSNPsNOINFO.txt]
  
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[https://dl.dropbox.com/u/13796643/fabry/seqbased/data/aa_properties.txt 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>, [https://dl.dropbox.com/u/13796643/fabry/seqbased/data/resMass.txt 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>,
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[https://dl.dropbox.com/u/13796643/fabry/seqbased/data/ip.txt 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>,
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[https://dl.dropbox.com/u/13796643/fabry/seqbased/data/pickedSNPsNOINFO.txt pickedSNPsNOINFO.txt]
   
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OUT: SNP_aaProps.txt, SNP_aaProps.wiki
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OUT: [https://dl.dropbox.com/u/13796643/fabry/seqbased/data/SNP_aaProps.txt SNP_aaProps.txt], [https://dl.dropbox.com/u/13796643/fabry/seqbased/data/SNP_aaProps.wiki SNP_aaProps.wiki]
 
perl [https://dl.dropbox.com/u/13796643/fabry/seqbased/scripts/read_AAProp.pl.html read_AAProp.pl]
  
perl [https://dl.dropbox.com/u/13796643/fabry/seqbased/scripts/read_AAProp.pl.html read_AAProp.pl]
   

Revision as of 10:23, 18 June 2012

Fabry Disease » Sequence-based mutation analysis » Journal

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 (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/>

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