BioEdit biological sequence alignment editor on Linux with Wine

Written by Tom Wickline

Wednesday, 31 October 2007 04:26

About BioEdit

BioEdit is a mouse-driven, easy-to-use sequence alignment editor and sequence analysis program designed and written by a graduate student who knows how frustrating and time consuming it can be to rely upon word-processors and command-line programs for sequence manipulation. BioEdit is intended to supply a single program that can handle most simple sequence and alignment editing and manipulation functions that researchers are likely to do on a daily basis, as well as a few basic sequences analyses.

Wine configuration

This is with a clean configuration directory and running in a 1024x768 virtual desktop.

$ winecfg

Once the .wine directory is built the configuration tool will start and you can set a virtual desktop in the graphics tab if you wish.

You will need to set odbc32 and odbccp32 to native (Windows) in the Libraries tab.

and the version that wine emulates to windows 98 in the Applications tab.

Installing BioEdit

Download Bioedit from here.

You will also need to download MDAC 2.5 SP3 from here.

Now to install MDAC 2.5 SP3

tom@tom:~$ wine mdac_typ.exe
fixme:midi:OSS_MidiInit Synthesizer supports MIDI in. Not yet supported.

BioEdit comes in a zip archive so just make a temporary directory and extract the distributed archive in it. then cd to this archive and run set.exe

tom@tom:~$ cd /home/tom/bioedit
tom@tom:~/bioedit$ wine setup.exe
fixme:advapi:LookupAccountNameW (null) L"tom" (nil) 0x34f80c (nil) 0x34f810 0x34f804 - stub

BioEdit first run

tom@tom:~$ cd /home/tom/.wine/drive_c/BioEdit
tom@tom:~/.wine/drive_c/BioEdit$ wine BioEdit.exe
fixme:midi:OSS_MidiInit Synthesizer supports MIDI in. Not yet supported.

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penncal 2009-06-29 17:43:44

Thank you! It worked like a charm with Wine 1.0.1 on Ubuntu 9.04.

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Nico1920 2009-09-02 06:23:56

It's crash when you try to align sequences using ClustalW Multiple alignment.

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ubuntu 10.09 2009-11-12 11:30:54

Thanks a lot, with ubuntu 10.09 and following this installation, BioEdit works fine for me. My
favourite functions, ClustalW and Create Local Protein Database File for BLAST also work ok. Some
minor problems with output format.

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ubuntu 10.09 2009-11-12 11:41:24

PS: The BioEdit version I installed was 7.0.9. It is just a bit slow.

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Tom Wickline 2009-11-12 13:03:08

Hello,

Hmmm, you could try turning off debug support and see if that helps the performance.

Example :

$ WINEDEBUG=-all wine BioEdit.exe

Tom

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Creating local nucleotide database

Diogo Silva 2010-02-08 02:45:52

Hi

I have a problem creating a local nucleotide database. I have ubuntu 9.10 and wine
v1.1.32.

There is no problem importing the database file but when I try to do a local blast, the
following error box pops up:

"Error reading queryBox->Lines.Strings: Richedit line insertion
error."

the .fas file I used for database doesn't seem to be the problem as I can open it
normally with bioedit. I also used the original file as well as a converted file using
"dos2unix" program, just in case the problem was about the text format in the file. None
worked so far.

If someone could please help, I would appreciate.

Thanks in advance
Diogo

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