How To Align Then Visualize The Alignment Of Rna Sequences With R Or Python

Question

[Abdullah]

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,

[gauravdube007]

Hey, ifreak can you please help me with this post?

Thanks in advance.

Answer 1

[Fabrice Jossinet]

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/ ?

[Abdullah]

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 ...

Answer 2

[Biojl]

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.

Answer 3

[Leandro Lima]

Maybe this can help/answer.

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

[Leandro Lima]

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