Genome Remapping Tool

Uploaded by NCBINLM on 23.02.2012

This video demonstrates how to use NCBI’s genome remapping tool. I’ll show you the
basics of how to remap annotation between different versions of the same assembly, but
you can also map features between different assemblies, for example, from the Venter assembly
to the human reference assembly. Cross-species mapping may be possible in the future.
The easiest way to find the Remap tool from the NCBI home page is to go to the Genome
database home page, then find the link to NCBI Remap under Genome Tools.
Let me first point out that answers to many questions about using Remap and how it works
are found through these links in the “NCBI Remap” box. And you can mouse over the question
mark icons to get explanations for specific options.
Let’s say I have a .gvf file - that’s the genome variation format - containing different
types of variations annotated on human genome build 35 (also called, hg17), and I’d like
to get the coordinates of these features on the current build, GRCh37.p5. This final selection
displays some statistics for the chosen assemblies.
You can then adjust program options in the next section, or proceed to the Data section.
I’ll paste in a small bit of my .gvf file, but you can also upload files. And let’s
say you just want the new coordinates for a small number of genes. In that case, paste
in the coordinates from your source record using a syntax like this...chromosome number,
colon, then gene coordinates separated by a dash or two periods. (chr15:72861768..72882558)
I’m ready to go, so I’ll click Submit.
I’m now on the Results page, where I have several options for viewing and downloading
various components of the remapping data. The Summary gives you a quick assessment of
the remapping process. The Mapping Report is partially displayed
here, but a Full Mapping Report contains much more information, such as the second pass
data, and every feature in the input file, whether or not it could be remapped. The downloaded
report is suitable for parsing or loading into Excel.
The Annotation Data contains only the features that map on the target assembly. It downloads
as a text file in the format specified on the input page, allowing you to load the remapped
features to most genome browsers. Lastly, you can export the data for viewing
and manipulation in NCBI’s Genome Workbench. This provides access to the assembly-assembly
alignments that were used to do the remapping.
That’s a quick tour of Remap. Please make use of the help links under NCBI Remap, and
use the “Write to the Help Desk” link to ask questions, offer suggestions, and report
any problems.