Using hexamers to predict cis-regulatory motifs in Drosophila

BMC Bioinformatics

Table 4 Potential novel CRMs predicted by HexDiff and other algorithms. All of the predicted CRMs listed in this table were predicted by HexDiff and at least two other algorithms. The column labeled "Gene" lists the gene involved in the early development of Drosophila that is closest to the predicted CRM. The columns labeled 1–5 are the different algorithms whose predictions matched the CRMs predicted by HexDiff: 1 – Ahab, 2 – Cluster Buster, 3 – MSCAN, 4 – MCAST, and 5 – LWF. The predicted CRMs were also compared to a compilation of 124 CRMs [32] – matching CRMs are listed in the last column.

Gene	Arm	Begin	End	Length	1	2	3	4	5	Matched
btd	X	9534921	9535192	271				*	*
eve	2R	5492385	5493575	1190				*	*	eve_late2_mel
fkh	3R	24421705	24422385	680				*	*
ftz	3R	2683060	2683406	346			*	*
gt	X	2268347	2270179	1832		*	*	*
gt	X	2290228	2290685	457	*	*	*	*	*	gt_23-bcd_mel
hb	3R	4503375	4503962	587			*	*	*
hb	3R	4519805	4520172	367			*	*
kni	3L	20628230	20628504	274	*	*	*	*		kni_+1_mel
prd	2L	12080435	12082316	1881	*			*	*	prd_bcd_mel
prd	2L	12089627	12089847	220				*	*	prd_1_mel
run	X	20488169	20488643	474	*	*	*	*
run	X	20524260	20524722	462		*	*	*	*
slp1	2L	3811050	3812092	1042				*	*
slp1	2L	3822581	3823049	468				*	*
slp1	2L	3824891	3825039	148	*	*	*	*	*	slp_A-bcd_mel
slp1	2L	3833433	3834671	1238		*	*	*	*	slp2_-3_mel
tll	3R	26680559	26683175	2616		*		*	*	tll_bcd_mel

ISSN: 1471-2105