It helps if you edit the sequences to start from the same base prior to importing them, that way if you do multiple sequences they are already mostly aligned. Make sure your mode is set to edit and insert. If you wish to keep them in the same order as they are in your directory then click on the bottom sequence file first, then click on the top one while holding the shift key. seq files exported from Chromas go File, Import, Sequence alignment file, browse to the correct directory, change file type to all, and select the files (.seq) exported from Chromas (in the open file box it often helps to change the view type to details, then click on type to group them all together). Note that I have changed or set many menu short cuts (see BioEdit stuff to change after installation below) to make things quicker, thus these instructions are based on these changes. Once I have edited all of my chromatograms I copy the. The reason why I paste them to a new file first is that importing from the clipboard (File, Import from Clipboard) will place them at the bottom of your file, which is usually not where I want them be. I then select those sequences (control-shift-a), cut (control-shift-c) or copy them (control-a) and paste them (control-s) to the desired BioEdit file. In the other copy of BioEdit I usually go File, New from Clipboard. If you need to copy and paste between copies of the program select the sequences, go Edit, Copy Sequences to clipboard (FASTA Format).
The regular copy and paste features work between copies of the program, but copying and pasting sequences does not.
One quirk of BioEdit is that if you double click a data file it will open in a new copy of BioEdit, not in an existing one. I would recommend saving everything in fasta format since that is the format I use in order to convert the data to another format or to another person (who probably doesn’t have a copy of BioEdit). As far as I can tell there is no difference between saving your file as a BioEdit formatted file versus as a fasta file. I use this feature on nearly every dataset I create. It is the only program I know of that allows you to edit, search and replace, and paste over the sequence title names independent of your sequences. Aside from that limitation (which isn’t as bad as it might sound once you learn a few tricks), I really like its features. The most annoying aspect is that you have to manually align up each sequence and manually create a consensus sequence (which commercial programs like Sequencher and Geneious are very good at).
#Chromatogram viewer sequencher free#
I use BioEdit to align sequences as it is free and has some handy features.
#Chromatogram viewer sequencher trial#
Each of the commercial versions have a free 60 day trial should you wish to try them. I’ve always used the free Chromas version, Chromas Lite, but there are two other versions with more features that are fairly cheap. One trick I find useful later is to always edit your sequences from the same starting base (unless the starts are all messy), as it makes sequence alignment much easier later. Alternatively, you can go edit, copy sequence, FASTA format and paste that into BioEdit. When I am done I save the chromatogram and export the data to a line file (which is saved with a. I usually make all of my edits as lower case bases as it makes it easier to identify where I have made edits. The chromatograms come off the machine with all bases in upper case. This opens the file in Chromas (see below under installation notes if some other program opens it instead of Chromas). MEGA also has an alignment editor, but I’ve not really used it very much.ĭouble click on the chromatogram file (usually has the extension ab1). BioEdit can also edit chromatograms, but I find Chromas to be nicer. If I loose my sequence alignment, at least all my chromatograms with the correct edits are still there to rebuild it from. Guide to editing sequences with Chromas and BioEdit Guide to editing sequences with Chromas and BioEditīy Peter Unmack Editing chromatograms with ChromasĬhromas has the advantage the you can save all of your chromatograms which can subsequently be used in any other programs unlike Sequencher which saves everything in a project file which cannot be opened by anything else.
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