During Blastin search, I found many sequences with Large sequence. (about 2105803 bp ). I faced a problem in adding them to DNA Alignment and in each time a message appeared "Warning: about to add protein sequences to DNA alignment. Please confirm". I would like to inquire how can I manage this message and when adding it to alignment there is no sequences added
I suppose you are using programs like MEGA to perform your alignment. Maybe you can use it on the command line in order to avoid your error message. But I think the length of your sequence is too large for this kind of programs. Maybe you could use Mauve, for larges alignments. But it depends on what and how you want to do it.
You should add more information about your problem.
http://darlinglab.org/mauve/mauve.html
Thanks a lot for all, I used MEGA 6 and my problem is I am unable to insert sequences from Blast-in search and all obtained sequences are large sequences and their nucleotide sequence is not edited in the flatfile record on GenBank. I tried to insert these sequences but their sequences were not insert on MEGA and the program sent the attached above message in my question. That is my problem
In order to MEGA recognize all your sequences, you need to have all these in one file before you run the alignment. If you just paste the sequences into MEGA, they might not be recognized. You can edit the file with the sequences by opening it with a text editor, or you can manipulate it from the command line. About the error message, check that you downloaded, the sequences you really need, maybe you are trying to join nucleotides and aminoacids sequences. However, I think you should try programs like Mauve, MAFFT, MUMmer or LastZ to perform your alignments.
we have developed a tool that is an hybrid between metaheuristics such as genetic algorithm. It deals with long alignments and runs parallel procesing.
The question is, what are you triyng to find from this alignment? a mean, along the sequences: are you searching for similar or identical regions? this simple question changes the result of the alignemnt process and other tools have no such tunning or setup
Dear Ernesto Rios Willars
I have 7 sequences for B. abortus and I need to do alignment for similar regions. Do sequences analysis comes in a parallel to bacteriological methods as standard identification tool in bacteriology.
Also, I found there is high identitiy among brucella spp., based on DNA sequences ranged from 97.3 to 100% for B. abortus, B. melitensis and B. suis, thus Is DNA sequences able to do like bacteriological methods and MLVA analysis that identified our isolates as B. melitensis.
For these variations, which one method we can depend in identification our isolates?
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