I sent some plant DNA for DNA sequencing and apparently, though sequences were sent back, some pairs don't create a consensus sequence. The sequencing company tried to re-sequence, bu to no avail. Will the available forward sequences still be useful for my phylogeny analyses? I still tried to edit the Forward sequences and do BLASTn searches and the results still show the expected type species. I hope someone can help. Thank you in advance.
Good morning,
the short answer is yes, even if you have only the forward sequence, this can work fine for your phylogenetic analysis.
A longer answer could be that shorter sequences (I assume having only the forward sequence makes them shorter?) carry less information, therefore your phylogenetic analysis might be a bit less informative than the same analysis on longer seqs.
A few questions to clarify the issue:
-how long was your expected sequence (forward + reverse) expected to be?
-how long is your forward sequence?
Cheers
Hey leigh
Yes, you can use it, but it depends on the quality and length of the sequences.
We commonly use re and fw sequences for two purposes: 1- to check the percision of each sequence and edit the ambiguous sites and 2- to make a consensus sequence without ambiguity.
Cheers
Francesco Martoni
Thank you very much for the insight and I apologize for the late reply. Apparently, we're able to resolve some of my sequences by re-sequencing. Though, I still need some help if it's okay?
This is with regards to my rbcL gene, the expected (forward+reverse) is around ~1300+ bp based on a previous study. However, since I only used universal primers, my samples only resulted to ~700+ bp.
In my analysis, will it be okay to combine my samples with 700 or less bp to those with 1300 bp, or should I trim it based on the results I got? Looking forward to your response.
Kiavash Golzarianpour
thank you for your response. I appreciate it. :)
- Badges
- Science method
- Similar topics
- Biological Science
- Evolutionary Biology
- Phylogenetics
- Phylogenetic Analysis