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Table 1 Results for the Drosophila melanogaster use case

From: LTRsift: a graphical user interface for semi-automatic classification and postprocessing of de novo detected LTR retrotransposons

Assigned family Reference family Number of candidates
dmel_1 mdg3 12
dmel_3 opus 18
dmel_4 copia 24
dmel_5 springer 6
dmel_6 Burdock 16
dmel_7 diver 8
dmel_8 HMS-Beagle 10
dmel_9 Tirant 19
dmel_10 Tabor 4
dmel_11 Quasimodo 14
dmel_12 Transpac 9
dmel_14 flea 16
dmel_17 invader2 8
dmel_17_2 invader3 7
dmel_18 Max-element 4
dmel_22 3S18 6
dmel_24 McClintock 4
dmel_26 Stalker 25
dmel_32 17.6 18
dmel_33 412 17
dmel_34 412 9
dmel_36 Idefix 5
dmel_39 rover 5
dmel_46 micropia 3
newfam_0 blood 25
newfam_29 HMS-Beagle2 4
newfam_40 297 20
manual gypsy4 7
manual mdg1 17
manual roo 94
  1. This table lists the putative families as assigned during our semi-automatic evaluation run on the Drosophila melanogaster genome (left column). The center column shows the name of the known family represented by that putative family, obtained from matching of the candidate sequence against a reference sequence set. The rightmost column lists the number of candidates in the respective family. The dmel_26 group (matched to various Stalker sequences) was not counted as recovered due to the multitude of non-unique matches to multiple references. Families with the newfam prefix were obtained by re-running the classification algorithm on subsets of the unclassified candidate set. Finally, families marked as manual were derived non-automatically.