Difference between revisions of "Fabry:Sequence-based mutation analysis/Journal"
Rackersederj (talk | contribs) (→Substitution matrices) |
Rackersederj (talk | contribs) (→Polyphen2) |
||
| Line 26: | Line 26: | ||
IN: pickedSNPsNOINFO.txt<br> |
IN: pickedSNPsNOINFO.txt<br> |
||
OUT: Polyphen.batch |
OUT: Polyphen.batch |
||
| − | perl prepBatchPolyphen2.pl |
+ | perl [http://dl.dropbox.com/u/13796643/fabry/seqbased_scripts/prepBatchPolyphen2.pl.html prepBatchPolyphen2.pl] |
=== SNAP === |
=== SNAP === |
||
Revision as of 09:04, 13 June 2012
Fabry Disease » Sequence-based mutation analysis » Journal
INSERT IMPORTANT AND INTELLIGENT STUFF RIGHT HERE
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
