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Old 06-08-2012, 07:49 AM   #7
pag
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Location: CA, USA

Join Date: May 2012
Posts: 72
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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
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