Forward and Reverse DNA Sequence Editing and Alignment
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- เผยแพร่เมื่อ 9 ต.ค. 2024
- This video tutorial explains editing and alignment of forward and reverse DNA sequences in Bioedit software. DNA sequence editing is an important step for quality and correctness of DNA data and thus the corresponding and final results.
#bioedit
#bioinformatics
#phylogentics
Firstly, thank you for your video. my question is why you paste the reverse sequence after the forward sequence ? my second question is can we do the multiple alignement in this case or not ? thank you
Nice video. I'm curious why you didn't build a consensus with both the forward and reverse sequences, rather you just paste the reverse sequence in front of the forward sequence. Don't you think that might lead to the wrong interpretation? considering that the position you pasted to is not necessary where the sequence would have merged with the forward sequence. Thanks!
Hi, Thanks! If you know how to do it manually, then you can better do it especially if your sequence data is difficult to work on it. Aligning both sequences manually need a bit info...that's ....always align poly-A head and tail with equal number of bases.
@@SCIRESEARCH Sir, I tried to align sequence according to your video. And when submitted those seq in GenBank, I got this response.
BLAST similarity search analysis indicates nearly all of these sequences
are misassembled at the 3' end.
This could be due to:
- a mixture of plus and minus strand sequence
- incorrect order of the assembled fragments
or
- missing sequence indicated by gaps in BLAST results
Thank you for this. I trimmed and generated the reverse complement. However, when I align the forward and reverse complement there are A LOT of mismatches. Am I doing something wrong?
Thankyou very much, you have demonstrated it very well. Mr. B Ali, as I read the user on the word file top, may kindly reply to this if he is admin of this channel. I have a few more questions to ask. TY
Hi! Thanks for your video. But I would like to ask if it is okay not to include the first nucleotide every time you select to copy a certain sequence like what you did. For example in your sequence, it starts with nucleotide "G" followed by "A" but when you copied and pasted it, the "G" was not included in the sequence but rather the "A" becomes first. Thanks again!
Thanks!! really helpful to understand reverse complement in Bioedit.
I guess I am quite randomly asking but does anyone know a good site to stream newly released tv shows online ?
@Kamdyn Brock i watch on Flixzone. You can find it on google =)
How about if i use 16s rRNA sequence, it mean i also have to put reverse? because RNA is one helix
Thank you. But my question is- Is it a consensus sequence? Can i submit this 1100b in genebank?
your Forward is 550 and Reverse is 550. if we make reverse complement of reverse then how you get 1100 rather than 550? Could you please describe me. thank you
Hi, to comment whether these are consensus sequences, I did not used my own sequences (e.g., ITS sequences we obtained from fungi) in this video. I took forward and reverse sequences from GenBank (I think belong to human gene)..so I can't say whether these are consensus or not. You can submit your sequences whether these consensus or not (provided you have good quality sequences with respect to size and alignment with query sequence). I'd used forward and reverse sequences and then I complemented these two sequences using reverse complement option in Bioedit (Of course you always need to complement your F and R sequences as scientific rule). For example you have two sequences F and R of 20 nucleotides size, so logically when you combine or add these two sequences it will give 40 KB. (However and generally the size of both sequences can vary depends on many factors such trimming during quality check) etc. I hope it make sense.
@@SCIRESEARCH Hello, Thank you for this helpful video. I have a similar question. I'm working with ITS region. Can i align both F and R on bioedit then ctrl+shift+r the R seq then select both to generate a consensus sequence?
Hello Sir. May I know how do I decide whether the sequence should be eliminate or use? Was it based on the peak?
Hi, there are some clues/signals that can helped you to figure out the quality of your sequence data. Important one is, the graph is the best interface to work on your sequence for quality check. Remember when you get sequences from sequence tech these sequences need your attention for correcteness (I would say you get raw data from sequence tech), of course you must eleminate unwanted data (e.g. ambiguous bases, many NNNN's), overlapped peaks etc. By the way from graph you can figure out which should be removed or intact. Hope it help you!!!
Sí, yo tampoco entiendo porque pega la cadena reversa complementaria al final de la cadena forward, no se tienen que alinear por el programa?
Thank you for sharing video. It was very helpful.
My pleasure!
Thank you very much! This was very helpful!
thanks, could you please give me some information about how to edit ambiguous bases in the same position on both reverse and forward sequences and also keep our mutations!
There are two ways to do it, either remove/delete the ambiguous base from any sequence (it won't affect on mutation positions), OR, second, keep the ambiguous bases, how? Replace the ambiguous bases with corresponding four bases,there is always a normal and correct base for ambiguous base. However, be careful with your sequence quality ....numerous ambiguous bases are not good and it affects on your whole sequence (size and quailty). So better to decide is this sequence need to discard or keep bases on quality threshold. Hope it make sense.
@@SCIRESEARCH thanks so much, I want to replace them with bases, and for example y is replaced by G and T, and my main question is which is the priority between these two main bases, and on what basis is the selection of a base between these two? (My sequences are sequences of drug-resistant patients, and I am looking for drug resistance mutations in the sequences)
@@janbibidorazehi3201 you can decide which base you want to add by looking to chromatograph or graph of the sequence and note the color of ambiguous base (color of signal or peak), there are four standard colors for each base (A, G, C, T) in any graph.
you are great sir, it's very helpful for me.
Thanks for sharing this great information
Thanks
Sir in NCBI after submitting the sequence an error occurred showing misassembled sequences. How to correct misassembled sequences? Please help
Can you tell me your sequences are assembled (you have aligned your forward and reverse sequences?), also tell me whether these are partial or complete sequences you're going to submit? After that, I hope I can help you out.
Why we r combining the F and RC sequences. We can align them to make a contig
Bz to show you have sequenced your segment from both directions ...5-3 .....3-5
Great work about sequneces
This was so helpful 😊
Thanks
Can you please suggest alternative of this for mac
Thanks!
Thanks a lot.
Well brother keep it up
Thanks
Very helpful
gracias por la traduccion bro
A1 sir
great work..tw
very nice ... tw
well done...tw
Where is your consensus??
You should never edit sequences in WORD - this is misleading!!!!!!!!
A1... tw
well.... tw
well....... tw
This is not right method
very helpful
very nice...tw