Table 3

Successful annotation based on BLAST against different gene collections

BLAST hits


Field

min E-valuea

Totalb

Bestc

Uniqued


Dmel.pro1

1e-171

1346

110.5

4

Dmel.nuc1

1e-147

264

7

6

Bmori.pro2

0e+00

1730

141.5

194

Bmori nuc2

0e+00

1265

1222

20

Bmori.wgs.nuc2

0e+00

1370

283

143

lep.nuc3

0e+00

1012

459.5

147

invert.pro3

1e-171

1488

170.5

4

NonRed.pro4

1e-175

1487

29

3

SwissP.pro4

1e-176

1136

25

1

organel.nuc5

3e-70

26

3

2

Rfam.nuc5

0e+00

27

2

0

plant.pro

1e-125

793

7.5

0

Ecoli.nuc

4e-12

7

1

1


a The threshold maximum E-value was set to 1e-05. b Total number of contigs with significant E-value. c Number of contigs having the lowest E-value for each specified BLAST field. When the lowest and second lowest E-values were the same for a particular contig it counted as 0.5 for each of the hit fields. d Number of contigs having significant BLAST hits exclusively for one of the fields. Some BLAST fields were combined to give the counts in Figure 2: 1 Dmel, 2 Bmori, 3 InvLep, 4 protein databases, 5 non-nuclear genes (as explained in the Methods). All collections used in our BLAST analysis were downloaded from public databases (see Methods) in June-August of 2005 (except for the organellar nucleotidic and the E. coli whole-genome sequences, both obtained in April 2004).

Beldade et al. BMC Genomics 2006 7:130   doi:10.1186/1471-2164-7-130

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