Comments (4)
@phycologia what are the flanking regions for this one?
I noticed a potential issue that would make it not find the start, but now I'm dealing with the ends not showing up. Can you confirm what the closing flanking region should be?
I find GACAA as a start (2 of them) and the matching end I have for that is '[AT]TGTC' which means either ATGTC or TTGTC, there is a ATGTC but 500 bases down so I don't think that's it. Am I missing one end for that?
@callmcgovern also check if this makes sense.
from cims-cyanobacterial-its-motif-slicer.
@nlabrad D1 begins with GACCT and ends with AGGTC
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Aha, I see it. And now I see what you mean. Maybe if there is more than one ITS starting pattern found we do something. Maybe if there is more than one and d1d1 is not found we try again, idk
from cims-cyanobacterial-its-motif-slicer.
@nlabrad @callmcgovern have we ever come across a sequence that doesn't have "AGGGA" right at the beginning of the ITS region? if that's always present then what if the code searched for "CCTCCT[TA]" followed by "(however you would code '2 or 3 variable bases')" followed by "AGGGA"? what's the range of leader sequence lengths we've seen? I think I've found only 7 & 8, but if it's sometimes longer then I guess it'd need to be a wider range of # of bases between CCTCCT[TA] and AGGGA
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Related Issues (20)
- snowella d1d1 illuminates an issue HOT 1
- New algorithm only returns results for first sequence in fasta file with many seqs HOT 1
- d1d1 length is "1" every time. HOT 1
- Do double output for Box B when needed. HOT 1
- can we make the script load dependecies automagically??
- Genbank -g argument not working. Returns "cannot parse this..." HOT 1
- Set limit to how long BoxB can be
- User specified flanking regions would help with accuracy if the user knows what to look for.
- BoxB truncated when script uses primary box b algorithm HOT 1
- BoxB sequences not found in fischerella spp HOT 1
- wrong boxb found with newest code HOT 9
- make length constraint for boxb on the small end HOT 1
- Changing naming of tRNAs HOT 1
- Change "motif search" to "CIMS" HOT 1
- quick fix for when using the -t flag HOT 1
- d1d1 is not outputting anything anymore... HOT 1
- cant save output file when using genbank fetch.
- synechococus and cynobium contain unique 16s ending and d1d1 beginning! HOT 8
- complete output wont save into text file if the sequence doesnt contain ITS regions HOT 1
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