puton bosc2010 bio_python-modules-rna
Post on 11-May-2015
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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/
BioPython – a set of freely available tools for biological computation written in Python.
http://biopython.org/
ACUGAUC
ACUGAUC
Adenosine (A) Uridine (U)
Cytidine (C)
Guanosine (G)
ACUGAUC
>>> from Bio.Alphabet.IUPAC import unambiguous_rna >>> from Bio.Seq import Seq
>>> seq = Seq(‘ACUGAUC’, unambiguous_rna)
ACUGAUC
>>> from Bio.Alphabet.IUPAC import unambiguous_rna >>> from Bio.Seq import Seq
>>> seq = Seq(‘ACUGAUC’, unambiguous_rna) >>> print seq.reverse_complement() GAUCAGU
Problem:
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There are 115 known post-transcriptionally modified nucleosides in RNA.
Moreover, several nomenclature schemes exist in parallel.
Known as: wybutosine yW Y 16G
http://github.com/krother/biopython branch rna_alphabet
$ git clone git://github.com/krother/biopython.git $ cd biopython $ git checkout rna_alphabet
Solution:
>>> from Bio.Alphabet.ModifiedRNAAlphabet import modified_rna >>> from Bio.RNA.RNASeq import RNASeq
$ python
Solution:
>>> from Bio.Alphabet.ModifiedRNAAlphabet import modified_rna >>> from Bio.RNA.RNASeq import RNASeq
>>> seq = RNASeq('AG:7CU', modified_rna)
$ python
Solution:
>>> 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
$ python
Solution:
>>> 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
$ python
Solution:
http://modomics.genesilico.pl/
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!
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
Thank you for attention!
Tomasz Puton t.puton@amu.edu.pl
Magdalena Rother lenam@amu.edu.pl
Kristian Rother krother@rubor.de
Janusz M. Bujnicki iamb@genesilico.pl
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