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 Sequences shorter than 360 bp and redundant sequences were removed with the vmatch program [21] (V.B. and S.K., unpublished), resulting in the reduced sequence set sizes given in the column 'Unique sequences'.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