Description: SynaMap™ accurately maps gene sequences (i.e. transcripts, genes and ESTs) onto a genome. It takes advantage of the exhaustive dynamic k-mer structure of SynaBASE™, which results in improved accuracy over fixed length k-mer indices as used by BLAT and BLAST. Exons missed by BLAT and BLAST are accurately and rapidly identified by SynaMap.

Application Example: Homo sapiens apolipoprotein L, 4 (APOL4) (NM_145660.1) was mapped to the Homo sapiens genome Build 36 v1 to discover the gene location and exons. SynaMap reports the location of 5 exons within 500 milliseconds. SynaMap identifies the position of the respective exons and reports putative splice sites in the correct order. The user has a choice of reviewing results in either the default user interface or as a GFF output which can be exported into downstream data mining packages. In this example, BLAT reports only 1 of the 5 exons for the gene, whilst BLASTN required significantly longer time and post processing exon identification to identify the 5 exons.

To try SynaMap, please:

1. Click here and then click on the “Access Now” button
2. Click on “SynaMap”.
3. Click on the ‘test sequence’ button and get the ‘Homo sapiens apolipoprotein L, 4 (APOL4)’ sequence fragment into the ‘Sequence’ box by clicking on the ‘Copy’ button.
4. The ‘Homo sapiens genome (NCBI Build 36 v1)’ SynaBASE should be selected.
5. Using the default parameters, click on ‘MAP’ to begin your analysis.