SynaMap™ is an application for accurately mapping the exon positions of a selected query sequence using SynaBASE patterns. SynaMap is also designed to recognize splice sites for more accurate mapping of exon positions within a particular genome.
A transcript variant of the Homo sapiens amyloid beta (A4) precursor protein (NM_000484.2), which plays a role in Alzheimer’s disease, was used to showcase SynaMap’s specificity by mapping against the Human genome. SynaMap was able to identify the positions of 18 exons on chromosome 21 in 401 milliseconds (Figure 1). In comparison, we have highlighted that BLASTN incorrectly reports 2 separate alignments for exons 1 and 6 (Table 1).
To try SynaMap, please:
Click here and then click on the “Access Now” button.
Click on the “Test Sequence” and get the Newsbyte test sequence labelled ‘Homo sapiens amyloid beta (A4)
precursor protein’ by clicking on the “Copy” button next to the sequence.
The ‘Homo sapiens genome (NCBI Build 36 v1)’ SynaBASE should be selected.
Using the default parameters given, click on ‘MAP’ to begin your analysis.
Figure 1: SynaMap results page showing the presence of 18 exons and their positions.
Table 1: The exon positions as reported by SynaMap and BLASTN where BLASTN reports two separate alignments for exons 1 and 6.