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