Tuesday, December 4, 2012

Fwd: Coordinate remapping service: NCBI

Not experienced enough to perform liftOver at command-line?

You can do it on the web in two places

* using Galaxy: https://main.g2.bx.psu.edu/

* at NCBI: http://www.ncbi.nlm.nih.gov/genome/tools/remapFwd: please follow footer link
Coordinate remapping service (NCBI Remap) is a tool that allows users to project annotation data from one coordinate system to another. This remapping (sometimes called 'liftover') uses genomic alignments to project features from one sequence to the other. For each feature on the source sequence, we perform a base by base analysis of each feature on the source sequence in order to project the feature through the alignment to the new sequence.

We support three variations of Remap. Assembly-Assembly allows the remapping of features from one assembly to another. RefSeqGene allows for the remapping of features from assembly sequences to RefSeqGene sequences (including transcript and protein sequences annoted on the RefSeqGene) or from RefSeqGene sequences to an assembly. Alt loci remap allows for the mapping of features between the Primary assembly and the alternate loci and Patches available for GRC assemblies.

You can view a short video describing how to use remap here: http://www.youtube.com/watch?v=0lhcMGGReVQ

(Original Post: http://www.ncbi.nlm.nih.gov/genome/tools/remap/docs/whatis.)