SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
How to fetch sequence from chromosome coordinates kumardeep Bioinformatics 6 05-29-2015 01:40 AM
Figure shows the coordinates in chromosome Rainbird Bioinformatics 1 06-23-2013 07:26 PM
Converting contig coordinates to genomic coordinates aurimas Bioinformatics 0 03-06-2013 11:06 AM
Chromosome start and end coordinates Ooinp Bioinformatics 1 04-23-2012 10:13 AM
Parsing a Chromosome sequence with start and end coordinates empyrean Bioinformatics 13 09-10-2011 09:23 PM

Reply
 
Thread Tools
Old 10-04-2013, 05:00 AM   #1
david.tamborero
Member
 
Location: spain

Join Date: Feb 2011
Posts: 60
Default Converting mRNA coordinates to chromosome coordinates

hi,

any of you know how to (easily) change mrna coordinates of a gene to chromosomal positions (or viceversa)? Something as (figures are invented): KRAS c.819A>T to chr12:25,357,800 A>T

I just need it from time to time in specific cases, so the simplest the better.

many thanks!
david
david.tamborero is offline   Reply With Quote
Old 10-04-2013, 05:11 AM   #2
dpryan
Devon Ryan
 
Location: Freiburg, Germany

Join Date: Jul 2011
Posts: 3,480
Default

Hopefully there's a website out there that will do that for you, but if not, you can use the transcriptLocs2refLocs() function in GenomicRanges (an R package from Bioconductor).
dpryan is offline   Reply With Quote
Old 10-04-2013, 05:41 AM   #3
david.tamborero
Member
 
Location: spain

Join Date: Feb 2011
Posts: 60
Default

Thanks for your answer!

FYI, the package -at least in my R libs installation- is in library('GenomicFeatures')

Anyway, I quickly check the command and it seems to require that I indicate the genomic coordinates of each exon (of each transcript) and therefore the position of the mrna I am interested in, so the 'only' thing that the program does is to use this info to perform the conversion.

I would love something that do not require to input more info than just the name of the gene and the mrna position...
david.tamborero is offline   Reply With Quote
Old 10-04-2013, 05:46 AM   #4
david.tamborero
Member
 
Location: spain

Join Date: Feb 2011
Posts: 60
Default

I mean, I notice that I can retrieve this info from another commands of the package, so I will do it (or using other means, as the Ensembl api) if no easier way to do that exists in some magic website or so.

thanks again!
david
david.tamborero is offline   Reply With Quote
Reply

Tags
dna coordinates

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 05:55 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO