Bioinformatics:Open Reading Frame (ORF)

Bioinformatics:Open Reading Frame (ORF)

The Open Reading Frame or (ORF) is a sequence of DNA located between the start-code sequence (initiation codon) and the stop-code sequence (termination codon).

The ORF finder softwares or algorithms are used to locate a gene in a given sequence by locating the initiation codon and the termination codon.

The initiation and termination codon can occur by chance so they could falsify our results, but in general the sequence found between them is not long enough, so to make sure its an ORF, we have to make sure that the sequence between the initiation and termination codon is long so it can represent a GENE.

The DNA sequence can be read in SIX different reading frames, 3 for each strand (because every codon have 3 bases).

In eucaryotic DNA we may find overlapping sequences withing a gene, these overlapping sequences are called INTRONS and they do not code for proteines.

Example: if we have a mRNA sequence:

1 st reading frame: AGUAAGAUGGCGAAUCUU
2 nd reading frame: - GUAAGAUGGCGAAUCUU
3 rd reading frame: - - UAAGAUGGCGAAUCUU

We can see that the first reading frame contains an initiation codon (AUG), the 2nd doesn't contain anything, the 3rd contains a stop codon (UAA).

So if we are about to choose a correct reading frame we would choose the first one.

There are many softwares dedicated for ORF detection, GeneMark is one of the best, it is a family of gene prediction programs developed at
Georgia Institute of Technology, Atlanta, Georgia, USA. You can access it from HERE.

Any questions you're welcome.

Bioinformatics:Bio Linux 5.0

Bioinformatics:Bio Linux 5.0

Bio Linux 5.0 is a project released in January 2009 for students and researchers in the field of Bioinformatics, it's a linux envirement (ubuntu) + more than 500 Bioinformatics programs with full documentation to each program.

This means that we can say that Bio Linux 5.0 is an easy to use Bioinformatics Workstation, powerful and easy to configure.

Bio Linux 5.0 is developed and maintained by the NERC Environmental Bioinformatics Centre, it contains a complete analysis and development environment easy to use by Bioinformaticiens.

Bio Linux 5.0 can run in a live DVD, that means that you can run it without installing it (without affecting your system), it can also run in a memory stick, You can install it in dual boot with Windows or in a virtual machine if you want to run it with Windows in the same time.

Above all of this Bio Linux 5.0 is FREE and you can download Bio Linux 5.0 from HERE

To access the NERC Environmental Bioinformatics Centre Homepage click HERE

If you already have an ubuntu system installed on your machine you can download Bio Linux 5.0 Packages from HERE and install them on your ubuntu, but i don't recommend that, because it takes more time and effort with less packages (Bio Perl, Bio Python...etc) not included in package repository, so the easy way is to download the full Bio Linux 5.0 and install it directly.

Any questions, please comment.