I have sequenced a 2.8 kb gene using sanger sequencing by generating overlapping primers.
I am trying to join the sequences to get a consensus sequence. I tried using multiple sequence alignment option in ugene. But the reverse reads dont seem to align even after I perform reverse complementation.
What can be done?
Before aligning your Sanger sequencing reads in UGENE, perform quality control to ensure accurate results. Terminal regions of reads often contain low-quality bases that misrepresent nucleotides, which can disrupt alignment. Trim these low-quality ends (e.g., Phred score
As well as Rakesh Sharma good answer check that the pcr or sequencing primers overlap the previous primer by at least 70 bases.....we get no usable sequence under the sequencing primer or for the next 30 bases at least
If you google search for "DNA sequence assembly software" you con find many commercial programs. Some offer a free 30-day trial. Surely there are also open-source or free programs available too, but I was not seeing many among the top hits in my Google search.
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