Wednesday, 10 April 2013

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.

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.

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.

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.

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.

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