Markup | Genome Research

Table 1.

Possible Novel Genes

Strand	Begin	End	`Genie`	`Genie EST`	`Genie ESTHOM`	Other gene-finder hits	Homology hits	Comments
F	21,599	21,988	X	—	—	5	0
F	131,015	131,248	X	X	X	5	0
F	267,633	268,061	X	X	X	1	0
R	306,476	306,985	X	X	X	1	0
R	328,048	328,733	X	X	X	4	0
F	329,808	331,184	X	X	X	6	0
F	403,468	405,391	X	X	X	5	2
F	408,759	412,000	X	X	X	6	2
R	426,746	427,525	X	X	X	6	0
R	603,442	604,456	—	X	X	5	0
F	754,773	754,919	X	X	X	2	0
R	846,339	845,892	—	X	X	3	0
R	870,684	870,866	X	X	X	4	0
R	910,572	911,055	X	X	X	5	0
F	1,115,807	1,116,493	X	X	X	2	0
F	1,117,474	1,117,608	X	X	X	3	0
R	1,263,535	1,264,137	—	X	X	3	0
R	1,365,077	1,365,732	X	X	X	4	0
R	1,850,650	1,851,240	X	X	X	4	0
F	2,453,955	2,454,498	—	X	X	4	0
F	2,580,916	2,581,059	X	X	X	1	0	possible FP
R	2,584,165	2,584,914	—	X	X	3	0
R	2,741,387	2,742,230	X	X	X	4	0
R	2,762,639	2,774,287	X	X	X	2	0
F	2,779,268	2,779,566	X	X	X	2	0
F	2,843,324	2,843,386	X	X	X	1	0	very short, possible FP

[i] Twenty-six Genie gene predictions that have no overlaps to any gene structure in std3. (Strand) The strand on which the predicted genes are located, consistent with the annotation inAshburner et al. (1999) “Genes on the top [forward strand] of each map are transcribed from distal to proximal (with respect to the telomere of chromosome are 2L); those on the bottom [reverse strand] are transcribed from proximal to distal.” Begin and End gene coordinates note the first and last base of the predicted coding gene region by Genie. Genie, GenieEST, andGenieESTHOM label the Genie program variant. (Other gene finder hits) The count of how often this newly predicted gene is also overlapped by one or more of the other six gene-finding programs. (Homology hits) The count of how often a newly predicted gene overlaps any homology hits.