Sequence editors for biologists on Linux
Sequence editors for biologists on Linux - Functions Print E-mail
Friday, 05 October 2007 09:10
Article Index
Sequence editors for biologists on Linux
Functions
Conclusion
All Pages
Page 2 of 3

Functions

I'll detail here the CLC Free Workbench's functions for DNA sequences. It also manages RNA and protein sequences, but does not feature specific functions for those that are not proposed for DNA.

Layout

DNA sequences may be displayed in two modes: a sequence and a map mode.

Image
Sequence layout
Image
Map layout

The software gives a nice look and feel and offers many display parameters to improve readability according to anyone's standards. My only disappointment was that linear DNA fragments may only be viewed as circular in map mode... Strange...

Restriction analyses

The main tool for molecular biologists will certainly be restriction analysis... which CLC Free Workbench does definitely well! It comes with a preloaded and quite comprehensive database of restriction enzymes which may be sorted by supplier, overhang types, "palindromicity" and popularity. Custom lists may be saved to improve work efficiency. Restriction sites are shown in the display pane with their names and overhangs while one will find the total number of sites for each enzymes in the settings pane.

Image
Restriction analysis

I guess the only preferences missing are a conditional display depending on the number of sites present in the considered sequence and highlighting of unique cutters in the display pane.

Alignements and philogeny

Alignements and philogenic trees are two basic features for molecular biologists. CLC Free Workbench's main weakness might reside here. Only simple tools are offered with only few options. The parameters for alignements are the traditional "gap opening" and "gap extension" and "gap closing" costs with two levels of accuracy. The user may choose neither a specific algorithm nor a specific score matrix. In conclusion, CLC Free Workbench's alignement tool and its depending phylogenic tree builber suffice for basic analyses, but might not be suitable for more careful bioinformatic analyses.

Image
Sequence alignement
Image
Phylogenic tree

ORF finding

The open reading frame (ORF) finding tool is also an essential. It is included in CLC Free Workbench and its output may be displayed in both layouts and saved in the "annotations" list of each sequence. The algorithm was updated in version 4.0.2 to correct a bug in ORF finding for circular DNA sequences.



Comments
Search
molgyk  - CLC free workbench 4.0.3   |2007-10-30 20:01:16
A new version (4.0.3) of CLC free workbench has been released mainly to fix some bugs. The installation procedure and the interface are still the same.
misha680  - Vector NTI runs very well in wine   |2007-12-13 07:17:33
Btw, thanks to some work myself and others have done in the previous year, Vector NTI actually runs very well in Wine, and this is definitely an alternative for people using Ubuntu. Basically, it's as simple as really just double-clicking on the installer if you have Wine installed (just "sudo aptitude install wine" first will do); if you'd like a little more of the tools menu (Web ordering) you'll have to dig around for mfc42.dll on google and (i) run "wine" with no parameters to create ~/.wine, (ii) copy mfc42.dll to ~/.wine/drive_c/windows/system32, and (iii) double-click on the installer. Only real big thing not working is online help. Hope this helps.
molgyk  - Thanks for the precision   |2007-12-13 13:33:11
I must say I only tried more than a year ago to run Vector NTi under Wine. By the time, it was not working as simply and I did not check for news since then. It's really good to hear that it may now be run under Linux! Thanks for the post.

A tiny question though: what version of Vector NTi runs now in Wine (if not all)?
misha680  - Which version?   |2008-01-15 00:27:00
Sorry didn't mention the version number. The latest that is downloadable from Invitrogen Vector NTI Advance 10 now works very well (perfectly except no online help index/searching, only context-based) on wine. I use it almost every day.
Geneious Developer  - Geneious doesn't only include a demo   |2008-04-08 07:03:20
When you download Geneious, it runs as Geneious Pro for 14 days and then reverts to Geneious Basic. You can continue to use Geneious Basic for as long as you want, so it's not just a demo as you say.

Also, unlike CLC the free version of Geneious will occasionally (about once in 8 days I think, but not in regular intervals) give you free use of the Pro features - it's called "Geneious Day".

Also, a new version 3.6.2 of Geneious is out and contains loads of new features and improvements.
molgyk  - Geneious   |2008-04-14 22:03:52
Thanks for the comment.

My post is becoming a bit old. Still, when I tested Geneious (I should have mentioned the version), I just thought the free "demo" version was not suitable for the simple everyday needs of a molecular biologist.

That said, I'll be glad to test the new features of Geneious soon!
Only registered users can write comments!

!joomlacomment 4.0 Copyright (C) 2009 Compojoom.com . All rights reserved."

< Prev
Last Updated on Friday, 03 July 2009 21:47