Assessing the impact of comparative genomic sequence data on the functional annotation of the Drosophilagenome

Table 4 Estimates of pairwise sequence conservation in coding and non-coding regions between D. melanogaster and D. erecta, D. pseudoobscura, D. willistoni or D. littoralis

Species	Number of bp surveyed	Number of bp conserved	% conserved (bp)	Median length of conserved segment	Average % identity of conserved segment
			Coding
D. erecta	63,655	60,327	94%	39	93%
D. pseudoobscura	46,626	26,978	61%	20	91%
D. willistoni	42,224	18,774	45%	17	91%
D. littoralis	19,717	10,997	63%	17	92%
			Non-coding
D. erecta	272,366	186,895	69%	24	94%
D. pseudoobscura	276,731	77,391	28%	17	95%
D. willistoni	174,421	19,700	13%	14	95%
D. littoralis	138,866	24,633	18%	15	95%
D. virilis	114,015	30,564	27%	16	95%
D. virilis [44]	114,015	29,915	26%	19	93%

Microsyntenic regions were globally aligned using AVID and conserved sequences greater than or equal to 10 bp and 90% identity were identified using VISTA. Sequences were classified as coding or non-coding using Release 3 annotations [14] exported from GadFly in VISTA format. Shown for comparison are a re-analysis of conservation between D. melanogaster and D. virilis using the current methods, as well as previous results, for a sample of non-coding regions published in [44].

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