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-   -   anyone who have used the software BioEdit before? (http://seqanswers.com/forums/showthread.php?t=16519)

bbsinfo 12-29-2011 06:54 AM

anyone who have used the software BioEdit before?
 
Hello, everyone. I am wondering whether anyone here has used BioEdit before to compare how similar two genomes are?
Recently, I have been trying to compare two organelle genomes by using this software, but I bumped into a snag, for some reason, I cant seem to be able to select two sequence files at the same time to tell the program to compare these two.
Anyone knows what I am talking about?

asheenlevrai 12-29-2011 10:18 AM

Hi,

I use bioedit (which is not maintained anymore), but only to compare short sequences (a few kb max). I usually align them manually but you can also use the clustalW plugin that is provided in "accessory application"

I usually copy paste my sequences as new sequences ("sequence"->"new sequence") and give each of them a name that will then appear on the left pannel. You can select multiple sequences by pressing the "shift" or the "control" key while selecting their names in the left pannel.
Shift key -> everything in between your 1st and last selection is selected.
Ctrl key -> only the items you select are selected.

I hope this is helpful.

good luck
-a-

bbsinfo 12-30-2011 10:16 AM

Hello, first of all, thank you so much for sharing all these with you.
I have two sequence that I saved seperately as two file.
I read the help file that to select two files , press shift key.
but my problem is that ,when i open both of my two files, there will be two windows, on the left pannel, in each window there is only one file name, the two file names could not be displayed in one window, together on the left pannel, I still could not select them both..
I am not sure whether you understand my problem...
If you understand, please please help
thanks

asheenlevrai 12-30-2011 12:06 PM

well, I think I see what you're doing.
You try to open your sequence files as if they were bioedit (alignment) files, using file->open or something, right?

In my hands, this does not work very well.

That's why I keep doing it the way I told you:
1) open a new (blank) bioedit file
2) open your 1st sequence in any viewer program (serial cloner 2-1 should be just fine).
3) copy your sequence (ctrl+c)
4) in bioedit, do : sequence->new sequence (popup window appears)
5) paste your sequence, add a name to it (in the corresponding field) and choose DNA (or something else) in the "type" field. Then press "apply and close"
6) repeat steps 2) to 5) for each of your sequences.
7) save your bioedit file!

This way, each sequence will be displayed as a single line with its name on the left pannel (you can reorder the sequence by dragging their name up and down in the list).

good luck
-a-

bbsinfo 01-03-2012 07:06 AM

Thank you so much for your helps. I think I finally could select more than one sequences in bioedit. I greatly appreciate your help.
So I run clustalW on my data, the score it gives me for example 75, means 75%of the two sequence is identical, right?
Good luck with ur research!! Thanks for taking the time to help me out. Noone in my lab used the bioedit before, without ur help, I dont know how long it is going to take me to figure out how to select more than one sequence at a time, :)

asheenlevrai 01-04-2012 08:01 AM

Quote:

Originally Posted by bbsinfo (Post 60766)
I greatly appreciate your help.
So I run clustalW on my data, the score it gives me for example 75, means 75%of the two sequence is identical, right?

I'm happy I could help.
I'm sorry but I am not so familiar with clustal and I don't want to give you inaccurate info. However you will probably easily get a confirmation online or in some clustal manual.

good luck for your research and happy new year.
-a-

pag 06-08-2012 07:49 AM

Sorry for resurrecting an old thread, but I may as well fill in some information being a frequent user of bioedit.

For nucleotides at least, I believe that you are correct - the score shows the identity between two sequences, at least within the aligned region. Low scores ( < 10 ) generally mean you should reverse-complement one of your sequences (and try again) or your sequences are very low quality. neither bioedit nor clustal will do reverse-complements of sequences automatically (in bioedit, the menu option is under "edit" rather than "sequences" I believe. - I do a "select all residues of selected sequence(s) from near the bottom of the edit menu and then a edit->nucleotide->reverse complement sequence. I have a modified bioedit.ini that I'd be willing to share that has these mapped to keyboard shortcuts so you don't have to wade through the huge menus.)

One thing BioEdit/Clustal won't handle is inversions and other rearrangements of the chromosome(s) from one species/clone to the next. For this application I would recommend (if neither genome is available on NCBI) creating a local BLAST database within BioEdit of one of your genomes. Then do a local BLAST against this with the other genome (check the box for tabular output). Then download and install Artemis Comparison Tool, save your table output from bioedit and import your altered sequence, then your blasttable file, then the reference genome into ACT.

For general use, in terms of getting two of your sequences open at once, you actually don't want to "open" the sequences. Go to BioEdit's file menu and select "new alignment". Then File->Import and import each of the sequences you wish to analyze (you can use control click, shift click or box select with the mouse if you wish). This, unfortunately does not bring with it the chromatograms or any such accessory info, but it does bring the raw sequence. If you have a 64-bit Windows operating system (8, 7, Vista, or XP) and you are importing from a file other than a .gb or .fasta, BioEdit may not be able to open the file directly, but will invoke readseq, which is an external application that you cannot configure. Unfortunately the readseq that comes with bioedit is not compatible with 64-bit operating systems, even in "compatibility mode". To get around this issue, download my patch at
http://code.google.com/p/readseq/downloads/list

http://code.google.com/p/readseq/ for more information

kaps 06-01-2015 03:25 AM

Quote:

Originally Posted by pag (Post 75711)
Sorry for resurrecting an old thread, but I may as well fill in some information being a frequent user of bioedit.

For nucleotides at least, I believe that you are correct - the score shows the identity between two sequences, at least within the aligned region. Low scores ( < 10 ) generally mean you should reverse-complement one of your sequences (and try again) or your sequences are very low quality. neither bioedit nor clustal will do reverse-complements of sequences automatically (in bioedit, the menu option is under "edit" rather than "sequences" I believe. - I do a "select all residues of selected sequence(s) from near the bottom of the edit menu and then a edit->nucleotide->reverse complement sequence. I have a modified bioedit.ini that I'd be willing to share that has these mapped to keyboard shortcuts so you don't have to wade through the huge menus.)

One thing BioEdit/Clustal won't handle is inversions and other rearrangements of the chromosome(s) from one species/clone to the next. For this application I would recommend (if neither genome is available on NCBI) creating a local BLAST database within BioEdit of one of your genomes. Then do a local BLAST against this with the other genome (check the box for tabular output). Then download and install Artemis Comparison Tool, save your table output from bioedit and import your altered sequence, then your blasttable file, then the reference genome into ACT.

For general use, in terms of getting two of your sequences open at once, you actually don't want to "open" the sequences. Go to BioEdit's file menu and select "new alignment". Then File->Import and import each of the sequences you wish to analyze (you can use control click, shift click or box select with the mouse if you wish). This, unfortunately does not bring with it the chromatograms or any such accessory info, but it does bring the raw sequence. If you have a 64-bit Windows operating system (8, 7, Vista, or XP) and you are importing from a file other than a .gb or .fasta, BioEdit may not be able to open the file directly, but will invoke readseq, which is an external application that you cannot configure. Unfortunately the readseq that comes with bioedit is not compatible with 64-bit operating systems, even in "compatibility mode". To get around this issue, download my patch at
http://code.google.com/p/readseq/downloads/list

http://code.google.com/p/readseq/ for more information

Hello,

I am using bioedit to do pairwise comparison of my sequences- then a pairwise seq matrix. Am not sure whether am following the steps well! here is how am doing it;
1. import seqs to bioedit
2. align with clustalW? when I do this some seqs are eliminated and only a few remain. Is this normal?
3. than alignment>sequence identity matrix
4. results.

I wonder if this is the right way?


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