[ensembl-dev] Ensembl ID History Converter (IDmapper.pl) API Mapping Score Column

Andy Yates ayates at ebi.ac.uk
Wed Jun 6 10:20:13 BST 2012

Hi there Lucas,

I'm sorry I missed answering this question in your original email. So the quick answer is the closer to 1 you are the better the mapping is. A mapping score of 1 means a 100% match.

As for how it's calculated it is generated from two sources; location based mapping and alignment based mapping on Exons. Location's score is based on the overlap two exons posses. Alignment's score is derived from an exonerate alignment where the score is (2 * match_length / (source_length + target_length)) with the ability to further modify this score depending on various other conditions (we prefer mappings which are located on the same sequence region). Once all scores have been generated we merge the two sets of results together for each exon pair which could be mapped and retain the highest score. Transcripts and Genes have their scores built from these Exons scores.

Hope this helps,


Andrew Yates                   Ensembl Core Software Project Leader
EMBL-EBI                       Tel: +44-(0)1223-492538
Wellcome Trust Genome Campus   Fax: +44-(0)1223-494468
Cambridge CB10 1SD, UK         http://www.ensembl.org/

On 2 Jun 2012, at 00:52, Lucas Swanson wrote:

> Hello,
> I am using the IDmapper.pl ID history converter to update some old gene IDs to the corresponding gene IDs in the current release.
> I am uncertain about the "Mapping score" column in the API output. What does it represent/how is it calculated, and is a higher number better, or is a lower number better?
> ~Thank you,
> Lucas Swanson
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