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Simon gp0

  • Germany
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View gist:4035fdac58a67f1fa669
  • Wir suchen zuerst mit BLAST (lokal, NCBI, oder EBI) nach Sequenzen S_i (i=1,...,n) in der PDB (d.h. Sequenzen zu denen bekannte Strukturen gehören), die ähnlich sind zu S_0. [BLAST ist Gegenstand der nächsten Vorlesung]

NCBI implementiert.

Modul: WebBLAST (Simon/Henning)

  • Die besten Hits (E-value < threshold) alinieren wir mit MAFFT.
View gist:a8e7d27edf979f8c0e0d
simon@t430 ~/.julia/v0.3/BiomolecularStructures $ julia src/PDB/pdb.jl
/usr/local/lib/python2.7/dist-packages/Bio/PDB/StructureBuilder.py:86: PDBConstructionWarning: WARNING: Chain A is discontinuous at line 5037.
PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/StructureBuilder.py:86: PDBConstructionWarning: WARNING: Chain B is discontinuous at line 5080.
PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/StructureBuilder.py:86: PDBConstructionWarning: WARNING: Chain C is discontinuous at line 5124.
PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/StructureBuilder.py:86: PDBConstructionWarning: WARNING: Chain D is discontinuous at line 5167.
PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/StructureBuilder.py:86: PDBConstructionWarning: WARNING: Chain A is discontinuous at line 5211.
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