ExTraMapper

ExTraMapper is a tool to find Exon and Transcript-level Mappings of a given pair of orthologous genes between two organisms using sequence conservation. The figure below shows the overall schematic description of ExTraMapper mapping the homologous transcript and exon-pairs between human and mouse genome.

Run ExtraMapper

Read all the configuration parameters first

source config.conf

export EXTRAMAPPER_DIR=$EXTRAMAPPERDIR

Set the liftover minimum match threshold

MAPPED_EXON_THRES=1.0

An example input gene pair (BRAF)

genePairId="ENSG00000157764-ENSMUSG00000002413"

Run ExTramapper (Requires python 2.7)

python $EXTRAMAPPER_DIR/scripts/ExTraMapper.py $MAPPED_EXON_THRES $org1 $org2 $genePairId > Outputs.txt