Puton bosc2010 bio_python-modules-rna
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This document discusses BioPython modules for handling RNA sequences containing modified nucleosides. There are 115 known post-transcriptionally modified nucleosides in RNA and several nomenclature schemes exist. The solution involves cloning a branch of the BioPython repository containing an RNA alphabet with modified nucleotides and using it to represent sequences containing modifications like 2-O-methyloadenosine. Example applications presented are ModeRNA for RNA structure modeling and CompaRNA for benchmarking RNA structure prediction methods, both of which use open source tools including BioPython.
![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](https://image.slidesharecdn.com/putonbosc2010biopython-modules-rna-100710215850-phpapp01/85/Puton-bosc2010-bio_python-modules-rna-11-320.jpg)
![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](https://image.slidesharecdn.com/putonbosc2010biopython-modules-rna-100710215850-phpapp01/85/Puton-bosc2010-bio_python-modules-rna-12-320.jpg)
Puton bosc2010 bio_python-modules-rna
- 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. BioPython – a set of freely available tools for biological computation written in Python. http://biopython.org/
- 3. ACUGAUC
- 4. Guanosine (G) ACUGAUC Cytidine (C) Adenosine (A) Uridine (U)
- 5. ACUGAUC >>> from Bio.Alphabet.IUPAC import unambiguous_rna >>> from Bio.Seq import Seq >>> seq = Seq(‘ACUGAUC’, unambiguous_rna)
- 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. 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. Solution: http://github.com/krother/biopython branch rna_alphabet $ git clone git://github.com/krother/biopython.git $ cd biopython $ git checkout rna_alphabet
- 9. Solution: $ python >>> from Bio.Alphabet.ModifiedRNAAlphabet import modified_rna >>> from Bio.RNA.RNASeq import RNASeq
- 10. Solution: $ python >>> from Bio.Alphabet.ModifiedRNAAlphabet import modified_rna >>> from Bio.RNA.RNASeq import RNASeq >>> seq = RNASeq('AG:7CU', modified_rna)
- 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. 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
- 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. 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. 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