Tuesday, 4 December 2012

NCBI Remap aka 'liftover' tool


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.

What's new

With the November 2012 update, we added the following features:
  • Alt locus remap: remap features between the primary assembly and the alternate loci/patches in GRC assemblies.
  • Clinical Remap: When you run this we will now make a call to the variation reporter and insert the results into Clincal Remap.
  • Added support for upload of compressed files. Currently GZip (.gz) and BZip2 (.bz) files are supported.
  • Improved HGVS nomenclature.

you can access the tool here 

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