Entering edit mode
9.3 years ago
allyson1115ar
▴
30
I would like to know how to read the position information output by BioProspector, MDscan and Weeder.
For example:
BioProspector
>chr3:49727648-49729655 seg 1 r58 -58 TCAAGTGATC
>chr3:49727648-49729655 seg 2 r194 -194 TCAAGCAATC
>chr11:73471365-73473372 seg 1 f296 -1713 TCAAGCGATT
r is reverse strand and f is forward strand in this case is that mean r58 start to count backward 58 bp? And the location information 49729655 - 58 = 49729597 as the reverse start position? Does this apply to MDscan as well?
MDscan
>chr8:145560414-145562421 St f247 CCGGGGGCGG
>chr8:145560414-145562421 St b361 CGCGGCGCGG
Weeder
310 + [TGAGATCA] 1844 (87.75)
310 - [TGATCTCA] 1844 (87.75)
310 - TGACCTCA 1091 (94.84)
May I know what does it mean by the given open and close bracket []? Is the position information same with bioprospector and mdscan? 1844 is the start position if for the case reverse strand - is the location start to count 1844bp from behind? I'm confused here. Explaination needed. Can anyone help me?
