FunctSNP: an R package to link SNPs to functional knowledge and dbAutoMaker: a suite of Perl scripts to build SNP databases

Table 4 Shows a summary of the output count after 4 program test runs

	Number of SNPs ...			Number of entries found in database for SNPs meeting input criteria ⁺⁺
#	meeting input criteria ^$$	derived from WGAS meeting criteria	found in database with score = > 20	Genes	Proteins	Pathways	Gene Ontology	Homologous Genes(with Homo sapiens)
1	165	165	1	52	23	43	259	47
2	7	7	1	7	4	19	29	5
3	15	1	8	15	9	29	114	13
4	11	0	11	6	10	21	126	6

# = test run number^$$ criteria determines the number of SNPs input into program
1: all 165 significant SNPs
2: significant SNPs with score greater than 7
3: SNPs with score greater than 11 within 10,000 base pairs from significant SNPs
4: SNP with score greater than 24 located on genes within 10,000 base pairs from significant SNPs.
⁺⁺ Example: For run 3, the highest scoring SNPs within 10,000 base pairs from 165 significant SNPs were found in database; 15 of the found SNPs met the criteria of score > 11; 1 out of the 15 SNPs found was a WGAS derived SNP; 8 SNPs from the 15 have a score = > 20. 15 SNPs are located on 15 genes with 9 protein products. The genes are involved in 29 pathways, have 114 Gene Ontology terms, and are homologous with 13 human genes.

ISSN: 1471-2105