Free Molecular Biology Tools - Part 1 of 3

I've been recently to a course covering Bio-Linux. It was quite a good starting point for an environment that apart from a few months dwelling on Ubuntu (on my own), was kind of an alien space for me. Well, it's not about Bio-Linux that I want to approach you guys, it's about the many tools one can find in the cyberspace these days, tools that eventually can represent a lot of spare time and better handling of high-throughput data. This course allowed me to learn a bunch whole of stuff concerning the Bio-Linux 7 system, as also gave me a nice perspective on the existence of different free tools that can help a biomolecular scientist work data in a much better fashion.

Let's go very quickly through a small list of different tools I managed to read about. Because NCBI has on its own a huge number of attached tools available for molecular biologists, I will talk about those some other time. Thus, I decided to list these ones according to the field they are more directly related to, but please feel free to comment on this distribution:

DNA Sequencing

(Geospiza's FinchTV)

Name: Geospiza's FinchTV
Summary: Popular chromatogram viewer for DNA sequence traces on Linux, Mac OSX, Windows and Solaris. 

Plus: Can display an entire trace in a scalable multi-pane view. Raw data views. Blast searching. Reverse complement sequences and traces.

Source: http://www.geospiza.com/Products/finchtv.shtml

Name: EMBOSS (The European Molecular Biology Open Software Suite)
Summary: Open source software analysis package specially developed for the needs of the molecular biology user community.
Plus: The software copes with data in a variety of formats, allows transparent retrieval of sequence data from the web, integrates a range of currently available packages and tools for sequence analysis.
Minus: The website displays a very confusing interface.
Source: http://emboss.sourceforge.net/

Name: Primer3
Summary: Widely used program for designing PCR primers.
Plus: Many different input parameters and easy to use.
Minus: A very pale and text oriented website.
Source: http://primer3.wi.mit.edu/


Name: Artemis
Summary: Free genome browser and annotation tool that allows visualisation of sequence features, next generation data and the results of analyses within the context of the sequence, and also its six-frame translation.
Plus: Written in JAVA, available for UNIX, Windows, Macintosh. Can read EMBL and Genbank database entries, can sequence in FASTA, GFF or even raw format.
Minus: It seems to me that know one really invests in an appealing website or interface.
Source: http://www.sanger.ac.uk/resources/software/artemis/

See you soon for the second and third part of this post. If you want to read more about these tools please visit Bioinformatics in Microbiology 2013.