Table 2.

Analysis of maize genome survey sequences: a comparison with maize proteins and ESTs

Approach	Number of entries	Unique sequences	wORF	Comparison with maize proteins					Reference
				%NS	%TE	%HP	%KP	NS %EST
Mutator insertions	4412	970	375	93	3	2	2	26	[26]
Random inserts	3480	2529	1015	61	38	1	1	44	[27]
Methylation filter	1692	1083	258	84	10	2	3	37	[28]
BAC ends	945	881	454	48	51	0	0	28	[29]
MPP	669	338	150	80	1	7	11	47	[30]
ORFs	399	86	79	76	0	14	10	22	[31]
Other	28	11	3	33	67	0	0	0

All sequences were retrieved from the GenBank GSS database (with the number of database entries given in the second column). Sequences shorter than 360 bp and redundant sequences were removed with the vmatch program [21] (V.B. and S.K., unpublished), resulting in the reduced sequence set sizes given in the column 'Unique sequences'. Of these, only sequences with non-redundant open reading frames of at least 120 codons (with the number of qualifying entries given in the wORF column) were compared to a maize protein set using BLASTP [23]. Entries were classified on the basis of BLASTP results and GenBank keywords as novel (NS), transposable element (TE), hypothetical protein (HP), or known protein (KP). The corresponding columns give the fraction of sequences in each class (percent). The column 'NS %EST' gives the percentage of sequences with novel ORFs matching maize ESTs. MPP, Missouri Mapping Project.