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NCBI Genome Remapping Service
This is a Beta-test version of coordinate remapping between genome assemblies and RefSeqGene sequences.
The following features have not yet been implemented but will be shortly:
full support for HGVS nomenclature (including c. nomenclature)
functional consequences of sequence changes
If there are other features you would like implemented, please let us know by filling out this
form
.
* indicates required fields.
Assembly-Assembly
Clinical Remap
We are sorry but a service supporting the Remap service is down. We expect this is a transient problem but if this persists, please use the
Write to the Help Desk
link to report the problem.
Genome Information
Source Organism *
Start typing to get a list of available organisms
Source Assembly *
Target Assembly *
Select the organism for which you wish to remap features.
Use the
Write to the Help Desk
to request an organism that is not in this list.
Select the assembly on which your data is annotated.
Use the
Write to the Help Desk
to request the addition of an assembly that is not in the list.
Select the assembly on which you wish to remap your features.
Use the
Write to the Help Desk
to request the addition of an assembly that is not in the list.
Alignments performed:
First Pass
Total
Percent Identity:
Percent Identity:
Remapping Options
Minimum ratio must be valid floating point number.
Minimum ratio of bases that must be remapped:
context specific help: Minimum ratio
Maximum ratio must be valid floating point number.
Maximum ratio for difference between source length and target length:
context specific help: Maximum ratio
Allow multiple locations to be returned:
context specific help: multiple locations
Merge Fragments:
context specific help: Merge Fragments
During the remapping,
what is the minimum amount of the feature that must be able to be remapped?
The default is 50%.
This metric allows for indels in the alignment.
If a feature is 100 bp on the source assembly, and it’s remapped length is 100 bp, this value is 1.
If there is a 1bp insertion in the target, this value is 1.1.
Regions of duplication often expand or contract between assemblies.
Checking this value will allow our second pass alignments (see the documentation) to be used and
remapping will be more robust in these regions.
If there is a small insertion in the target assembly such that a feature would remap to two locations,
this feature allows these features to be merged so that only one feature is in the annotation file.
Genome Information
Available only for human
I have data on *
I want to map data to *
Remapping Options
Define RefSeqGenes
Map to any available RefSeqGene sequence
Map only to the RefSeqGenes I specify
Not all regions of the genome have RefSeqGenes.
You can choose to get data for any available RefSeqGene or only specific ones. To request a RefSeqGene for a gene click
here
Please upload a file or paste data here *
Upload a list of accessions or Gene names:
OR
Paste:
You can paste multiple lines into the text area.
Define Transcripts/Proteins
Provide locations on NMs/NPs associated
with RefSeqGenes
Provide locations on NMs/NPs even if there is no RefSeqGene
NCBI Remap
What is NCBI Remap?
About our alignments
FAQ
API Documentation
About Genome Workbench
Write to the Help Desk
Data
Input format:
Best Guess
HGVS
BED
GVF
GFF
GTF
GFF3
Text ASN.1
Binary ASN.1
UCSC Region
VCF
context specific help: input format
Output format:
Same as input
HGVS
BED
GVF
GFF
GTF
GFF3
Text ASN.1
Binary ASN.1
UCSC Region
VCF
context specific help: output format
Please upload a file or paste data here *
Upload a file:
OR
Paste data here:
You can paste multiple lines into the text area.
You can specify the format your file is in, or you can just let us guess.
You can specify the format in which you want the remapped annotations to be produced.
The default is to produce the format as the original features.
Problems
The submit button below is disabled because your input is not yet complete. Please correct these problems above.
Submit
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