Table 2

Efficacy of partial ORF linkagea

Strain

True matching fragments linked (%)

False matching fragments linked (%)b


S. albus J1074

127 (22.1)

2 (0.4)

S. clavuligerus ATCC27064 (#1)

58 (31.2)

0 (0)

S. clavuligerus ATCC27064 (#2)

40 (9.3)

0 (0)

S. clavuligerus ATCC27064 (#3)

12 (20.7)

2 (3.5)

S. ghanaensis ATCC14672

182 (28.04

0 (0)

S. griseoflavus Tü4000

326 (27.5)

2 (0.2)

S. hygroscopicus ATCC53653

220 (20.2)

1 (0.1)

S. lividans TK24

117 (27.9)

2 (0.5)

S. pristinaespiralis ATCC25486

207 (20.7)

0 (0)

S. roseosporus NRRL11379

182 (46.2)

7 (1.8)

S. roseosporus NRRL15998

192 (41.6)

8 (1.7)

Streptomyces sp. XylebKG-1

0 (0)

0 (0)

Streptomyces sp. C

146 (17.9)

9 (1.1)

Streptomyces sp. e14

158 (17.7)

2 (0.2)

Streptomyces sp. Mg1

46 (12.0)

0 (0)

Streptomyces sp. PP-C42

887 (10.6)

No scaffolds

Streptomyces sp. SPB74

145 (15.8)

12 (1.3)

Streptomyces sp. SPB78

109 (12.8)

6 (0.7)

S. sviceus ATCC29083

200 (28.1)

7 (1.0)

S. viridochromogenes DSM40736

102 (31.1)

8 (2.4)


a All Streptomyces genomes except Streptomyces sp. PP-C42 and each query genome were used to link partial ORFs in that query genome. The parameters used were: ≥ 20% identity to and ≥ 60% coverage between the query and reference sequence and ≥ 50% similarity between the identities of each partial fragment to the reference sequence.

bFalse positive linkages were identified from their incongruencies with the scaffold information

Klassen and Currie BMC Genomics 2012 13:14   doi:10.1186/1471-2164-13-14

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