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Table 2 Analysis of maize genome survey sequences: a comparison with maize proteins and ESTs

From: Comparative genomics of Arabidopsisand maize: prospects and limitations

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

 
  1. 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 Sequences shorter than 360 bp and redundant sequences were removed with the vmatch program [21] (V.B. and S.K., unpublished), resulting in the reduced sequence set sizes given in the column 'Unique sequences'.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.