Puton bosc2010 bio_python-modules-rna

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Puton bosc2010 bio_python-modules-rna

  1. 1. BioPython modules for handling RNA sequences containing modified nucleosides. Tomasz Puton, Kristian Rother, Magdalena Rother, Janusz M. Bujnicki Laboratory of Structural Bioinformatics Adam Mickiewicz University, Poznań, Poland http://bioinformatics.amu.edu.pl/Lab/ International Institute of Molecular and Cell Biology Warsaw, Poland http://iimcb.genesilico.pl/
  2. 2. BioPython – a set of freely available tools for biological computation written in Python. http://biopython.org/
  3. 3. ACUGAUC
  4. 4. Guanosine (G) ACUGAUC Cytidine (C) Adenosine (A) Uridine (U)
  5. 5. ACUGAUC >>> from Bio.Alphabet.IUPAC import unambiguous_rna >>> from Bio.Seq import Seq >>> seq = Seq(‘ACUGAUC’, unambiguous_rna)
  6. 6. ACUGAUC >>> from Bio.Alphabet.IUPAC import unambiguous_rna >>> from Bio.Seq import Seq >>> seq = Seq(‘ACUGAUC’, unambiguous_rna) >>> print seq.reverse_complement() GAUCAGU
  7. 7. Problem: The linked image cannot be displayed. The file may have been moved, renamed, or deleted. Verify that the link points to the correct file and location. There are 115 known post- transcriptionally modified nucleosides in RNA. Known as: Moreover, several nomenclature  wybutosine schemes exist in parallel.  yW  Y  16G
  8. 8. Solution: http://github.com/krother/biopython branch rna_alphabet $ git clone git://github.com/krother/biopython.git $ cd biopython $ git checkout rna_alphabet
  9. 9. Solution: $ python >>> from Bio.Alphabet.ModifiedRNAAlphabet import modified_rna >>> from Bio.RNA.RNASeq import RNASeq
  10. 10. Solution: $ python >>> from Bio.Alphabet.ModifiedRNAAlphabet import modified_rna >>> from Bio.RNA.RNASeq import RNASeq >>> seq = RNASeq('AG:7CU', modified_rna)
  11. 11. Solution: $ python >>> from Bio.Alphabet.ModifiedRNAAlphabet import modified_rna >>> from Bio.RNA.RNASeq import RNASeq >>> seq = RNASeq('AG:7CU', modified_rna) >>> print seq[2].full_name 2-O-methyloadenosine
  12. 12. Solution: $ python >>> from Bio.Alphabet.ModifiedRNAAlphabet import modified_rna >>> from Bio.RNA.RNASeq import RNASeq >>> seq = RNASeq('AG:7CU', modified_rna) >>> print seq[2].full_name 2-O-methyloadenosine >>> print seq[3].long_abbrev m7G
  13. 13. http://modomics.genesilico.pl/
  14. 14. Example applications (part 1): ModeRNA: A tool for comparative modeling of RNA 3D structure. http://iimcb.genesilico.pl/moderna/ Our software models modified RNA 3D structures! Open source project!
  15. 15. Example applications (part 2): CompaRNA: A server for continuous benchmarking of automated methods for RNA structure prediction POSTER NUMBER: W17 SUNDAY, JULY 11: 12:40 p.m. – 2.30 p.m. http://comparna.amu.edu.pl/ Uses open source software e.g. BioPython, PyCogent & ModeRNA
  16. 16. Thank you for attention! Tomasz Puton Kristian Rother t.puton@amu.edu.pl krother@rubor.de Magdalena Rother Janusz M. Bujnicki lenam@amu.edu.pl iamb@genesilico.pl

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