Checking Failed Plasmdisaurus Seqencing By BLASTing Reads
No parameters, just looking for the closest sequence.
Read 1 best hit: D. virilis ribosomal RNA
Read 2 best hit: D. virilis glucose dehydrgoenase
Read 3 best hit: D. virilis clone sequence
Read 4 best hit: mamailian expression vector pCAGGS
Read 5 best hit: D. virilis mRNA
Read 6 best hit: D. virilis mdG4 gene
Read 7 best hit: D. virilis golgi protein
Read 8 best hit: D. virilis protein
Read 9 best hit: D. virilis protein
Read 10 best hit: D. virilis protein
Read 11 best hit: just repeats
Read 12 best hit: just repeats
Read 13 best hit: just repeats
Read 14 best hit: D. melanogaster 3R
Read 15 best hit: D. novoamexicana protein
Read 16 best hit: NA
Read 17 best hit: NA
Read 18 best hit: NA
Read 19 best hit: E. coli
Read 20 best hit: common barbel (fish)
Read 21 best hit: NA
Read 22 best hit: just repeats
Read 23 best hit: D. buskii
Read 24 best hit: D. virilis protein
Read 25 best hit: D. virilis ribosomal RNA
Read 26 best hit: D. virilis protein
Read 27 best hit: Giant abalone DNA
At this point I stopped because all of this is just crap!! This probably means my extraction didn’t work at all, because there seems to be no plasmid DNA in there, except for 1 read but I don’t know if I trust it.
I also ran the extraction on a gel to see if it was the expected size. It’s not! It’s supposed to be 14,000bp, but it looks larger than 20,000bp.
