I want to generate a consensus DNA sequence from F and R sequences with Bioedit. I had first inverted the R and F sequences using the reverse complement pull down menu. Then, I aligned them with the accessory application pull down menu and used the alignment: plot identities to first sequence with a dot pull down menu to highlight sites where all the sequences are identical. How can i interpret the results and generate my consensus sequence?
In general you may to generate consensus sequence in the next way: select all your dataset, than align your sequences (Accessory application -> ClutalW multiple alignment). After this you may select all sequences you want to built consensus, than choose Alignment -> Create Consensus Sequence. Than you would have consensus. Non synonimous positions will be named in according to IUPAC nomenclature.
Just add on to that what Andrii said: Important is that if you have the consensus sequence that you look into the raw data again in order to check the peaks of your non synonymous bases to make a final decision which base you keep (or if you have re-sequence this area again). This occurs usually only (if the sequences were high quality produced) at the beginning of the sequence where the (taq) polymerasis is amplifying. (5'->3'). Hope that helps.
Sounds like you are looking to assemble the 2 reads versus making a consensus sequence. I.e., the consensus should be 100% agreement between the 2. As mentioned in previous responses, you need to examine the raw data to determine how far the peaks are reliable. The first 20-40 may be unreliable, but hopefully your reverse seq will run past that. On the other ends, hopefully you can find your primer seq and cut that off. Depends on fragment length and the length of read.
Good luck
Dear Sir,
I appreciate to know how to transform aligned sequences in Bioedit program to microsoft word or how to print?
Regards
Oumed
You can print your alignment from BioEdit directly. Why you need MS Word for it?
Dear Andrii
Thanks I need to copy aligned sequences to microsoft word when I want to write a manuscript can you help?
Also when I want to transfer aligned sequences it become out of focus this is true for Mega 5 aligned sequences!
In mega aligning software when you print directy the phylogram will be printed in 5-10 pages, I need to print them in 1 page, how?
You need to put all alignment on one sheet or only the part of alignment?
Hi, I'm using the MAFFT program on the EBI website (http://www.ebi.ac.uk/Tools/msa/mafft/) to do my alignment (!! select in STEP 2 : ouput format : Clustal W !!). And then I just copy-paste it on word. Sometimes I need to make some small modifications in word (remove some spaces or line feed) but it's perfect for publication. I hope it helps!
Once I have my aligned sequence in BioEdit, I select File, then Graphic View. It opens a window called Graphic Print: Untitled. In this window, you can select your shading and identity threshold. I then select Edit, then copy page as a bitmap. Then I paste it into my next document.
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