Hi everyone, I have forward and reverse sequences of 16S region from my sample (Sanger), and I was editing them on MEGA (latest version 11), by getting rid of the noise/tails, reversing the complement and finally align them. At this point, however, I got stuck, since I can't figure out a way to make the consensus sequence or export it somehow. So far I've only found the command 'Concatenate', but I'm not sure it's the right one to make the contig.
I can of course use other freewares (e.g. BioEdit), but I just want to know how to do it directly on MEGA, if it's possible, since I'm going to use it for downstream phylogenetic analyses etc.
Many thanks in advance
Probably Mothur (https://mothur.org/wiki/consensus.seqs/) can help you with that. The software is available for all operating systems and is very intuitive. You would only need to save your fasta alignment from MEGA. If you have trouble running mothur, you can use any of these online tools:
https://gene-calc.pl/sequences-analysis-tools/consensus-sequence
https://www.bioinformatics.nl/cgi-bin/emboss/cons
Hi Jose, thanks for the answer. I was looking a way to do it directly on MEGA, I can check mothur as well.
Mara Simonazzi
Just follow two simple steps;
Step 1: Open your raw sequence file on Chromas software, check your sequence by doing BLAST, and save the file as an SCF file for both forward and reverse sequences separately.
Step 2: Use SeqMan: Add both forward and reverse SCF files on SeqMan, it will generate a consensus sequence then save your current session as a contig.
Step 1: Chromas
http://technelysium.com.au/wp/chromas/
Step 2: SeqMan
https://www.dnastar.com/workflows/sanger-sequence-assembly/
Hi Mojnu Miah Thanks for your comments.
I would like to check heterozygosity in sanger sequencing. Can you suggest me any software which can simply do it? Thanks in advance.
Hello Mara Simonazzi, I'm having your problem right now, did you find a way to generate or somehow export the consensus thread?
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