Question: How To Align Then Visualize The Alignment Of Rna Sequences With R Or Python
0
gravatar for Abdullah
6.6 years ago by
Abdullah100
Germany
Abdullah100 wrote:

Hi,

I have two RNA-sequences along with there bracket annotation ..

i have 2 questions:

  1. is it possible to align then inside R??
  2. if i already have the alignment outside R, is there anyway to present it in a colrful way such to show the matched pairs, the gaps, the non-matched pairs in different colors ..

i can align the sequences inside python, but i'm not sure if there is a good way to perform this inside python, so the question would be in R or python...

Regards,

R alignment • 3.3k views
ADD COMMENTlink modified 6.6 years ago by Leandro Lima930 • written 6.6 years ago by Abdullah100

Hey,ifreakcan you please  help me with this post ??

Can Anyone Suggest Me A Program For Converting Dot-Bracket Notation Format To Standard Hybridization Format.

Thanks in advance.

ADD REPLYlink modified 5.4 years ago • written 5.4 years ago by gauravdube0070
1
gravatar for Fabrice Jossinet
6.6 years ago by
Strasbourg, France
Fabrice Jossinet150 wrote:

Hi,

Answer 1: i would call an external command to compute such alignment and recover the result from R.

Answer 2: ok, this is neither R nor Python, but what about Ralee (an emacs plugin):http://personalpages.manchester.ac.uk/staff/sam.griffiths-jones/software/ralee/ ?

ADD COMMENTlink written 6.6 years ago by Fabrice Jossinet150

seems like a good idea ... but what i want is something more dynamic that can be included into a script, because i want to do this for a lot of alignments ...

ADD REPLYlink written 6.6 years ago by Abdullah100
1
gravatar for Biojl
6.6 years ago by
Biojl1.7k
Barcelona
Biojl1.7k wrote:

You can align them using MAFFT or PRANK calling them from a R/python/perl/younameit script. To view alignments and generate figures I particularly like jalview:http://www.jalview.org/ It has a lot of different view options.

ADD COMMENTlink written 6.6 years ago by Biojl1.7k
1
gravatar for Leandro Lima
6.6 years ago by
Leandro Lima930
San Francisco, CA
Leandro Lima930 wrote:

Maybe this can help/answer.

http://www.bioconductor.org/help/workflows/high-throughput-sequencing/

ADD COMMENTlink written 6.6 years ago by Leandro Lima930

Or this: http://cran.r-project.org/web/packages/seqinr/index.html

ADD REPLYlink written 6.6 years ago by Leandro Lima930
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