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What kind of software tool would you recommend as best suited to detect psbA-trnH inverisons? I have 1x coverage Sanger .fasta files and >2000 sequences, with 1 sequence per species. Most tools I have found are only suitable for next generation seuqncing data or inversions that are larger than 50 bp.

Here is an example: enter image description here

enter image description here

(dotted line)

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  • $\begingroup$ Please edit your question and highlight the precise inversion you are looking for. I know you've shown us the relevant region but what is the "non-inversed" sequence and what is the inversed one? I don't see anything obvious in your alignment. $\endgroup$ – terdon Feb 9 '17 at 11:22
  • $\begingroup$ The inversion is where the dotted line is, for example. Non-inversed is TTCTAG and inversed is CTAGAA. I don't know what I am looking for, that is what the question is about. I need to find the inversion. The pictures are just examples of what it could look like. $\endgroup$ – user5878028 Feb 9 '17 at 11:33
  • $\begingroup$ Yes, that much I understood :) However, since you've posted an image and not an actual alignment (not text that I can copy and investigate), we need more detail. I can't see what the inversion is and what the reference is. You also show two separate alignments with completely different regions marked. Your second seems to be referring to 5nt while your first to more than 20. $\endgroup$ – terdon Feb 9 '17 at 11:37
  • $\begingroup$ Yes exactly, I have 10000 sequences across all plant families and I don't know which length or which positons the inversions have, or if they exist at all. That's why I need help to find them. Maybe there is a tool that I am not aware of. Posting an alignment is not possible, because the standard alignment tools do not align this region, it gets spaced out, because it looks very diverse, however it's not. Alignments seen above are corrected by hand. $\endgroup$ – user5878028 Feb 9 '17 at 17:30

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