Bioinformatics: Genomics: Different Types of RNAs

Bioinformatics: Genomics: Different Types of RNAs

RNAs are macromolecules which plays a major and necessary role in biology, they play a role of intermediary between DNA and Proteines .

RNAs can fold to secondary and even tertiary structures.

The main purpose to study RNAs in bioinformatics is to try to predict their structures, to know better about their interactions and their stability.

You can read about RNA structures in this post HERE.

RNAs have 2 main types:

1- Coding RNAs: Corresponding to mRNA (Messenger RNA) that plays a role of a transmitter, which transmits information from RNA and deliver it to Protein.

2- Non coding RNAs: Like rRNA (Ribosomal RNA), tRNA (Transfer RNA), snRNA...etc



mRNA : messenger RNA.
rRNA : ribosomal RNA.
tRNA : transfer RNA.
snRNA : (small nuclear) .
snoRNA : (small nucleolar ) .
scRNA : small cytoplasmic RNA.
tmRNA : transfer-messenger RNA.
siARN : small interfering RNA.

Any comments you're welcome.

Bioinformatics: Genomics: RNA secondary structure

Bioinformatics: Genomics: RNA secondary structure

As proteins can have a complex structures, RNAs too, because a major advance in biology in the 1970s had shown that RNAs can have a complex 2D and even 3D structures.

The good thing to hear is that RNAs obey folding patterns or laws that are much simpler then the complex protein folding laws.

In order for an RNA molecule to work, it has to be protected from solvents, to do that, RNA bases pair themselves with other bases, this pairing forms RNA secondary structure.

When the two RNA stretches (we're talking about one RNA molecule) are perfectly compatible, or complementary to each other, they form what's called STEM.

Note: STEMs don't have to be 100% compatible, so we can find also unpaired residues.

When the stretches aren't compatible they form what's called a LOOP.

Tertiary interactions may also occur in an RNA molecule, but its very difficult to predict there tertiary interactions.

Any comments you're welcome.

Bioinformatics: Main Applications Of Multiple sequence Alignment

Bioinformatics: Main Applications Of Multiple sequence Alignment

You can read an introductory post to Multiple Sequence Alignment HERE, to understand what is a Multiple Sequence Alignment.

Multiple Sequence Alignment is almost the most useful tool in Bioinlformatics, it helps almost in every application of Bioinformatics (predicting protein structure, predicting protein function, phylogenetic analysis...etc).

The main applications of Multiple Sequence Alignment are:

1- Structure Prediction: a Multiple Sequence Alignment can give you the almost perfect protein or RNA secondary structure, some times it helps even with the 3D structure.

2- Protein Family: a Multiple Sequence Alignment can help you to decide that your protein is a member of a known protein family or not.

3- Pattern Identification: By looking at conserved regions or sites, you can identify which region is responsible for a functional site.

4- Domain Identification: By looking at file provided by a Multiple Sequence Alignment, you can extract profiles to use them against databases.

5- DNA Regulatory Elements: You can use Multiple Sequence Alignments to locate DNA regulatory elements such as binding sites...etc.

6- Phylogenetic Analysis: By carefully picking related sequences you can reconstruct a tree using sequences that u have used in the Multiple Sequence Alignment (You can use the PHYLIP package and you can find a post about it here).

As Multiple Sequence Alignments are playing a major role in Bioinformatics, you can use it almost anywhere but as every thing on this earth, nothing is perfect or 100% accurate, so u have to choose your sequences very carefully to prevent meaningless results.

You can access the EBI ClustalW program from HERE, to do a Multiple Sequence Alignment.

Any comments you're welcome.

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: Swine Flu Genome:

Bioinformatics: Swine Flu Genome:

The swine flu A (H1N1) virus is an RNA virus that codes 8 genes, its Genome is composed of avian flu, human flu Type A, human flu Type B, Asian swine flu, and European swine flu, this combination is supposed to be rare and have only a chance of less than 0.1 to be a natural event.

The two anti-viral drugs Tamiflu and Relenza are availible on the market and can lessen the symptoms of swine flu.

But the Swine Flu virus has made some sort of resistance to Tamiflu and the % of resistance is growing now.

Now all submitted influenza sequences are availible at GenBank and are availible for Blast searching at NCBI here , with a set of tools that you can use to analyse the sequences.

So we hope that the cure will be found before the next mutation of the virus.

Bioinformatics:Genomics:Microarrays

Bioinformatics:Genomics:Microarrays:


Microarrays are micro-chips used in molecular biology and medecine to achieve a lot of useful tests including gene expression.

To inderstand this technology, we should put a thing in our minds, wich is:
1- Not all the genome codes for proteines.
2- Not all genes always turned on.

We use the term Gene Expression to describe the transcription of the information containes within the DNA into mRNA, which is after translated to proteines.

Scientists have to study these genes to identify which of theme are expressed and which are not.

Gene expression is a highly complex and tightly regulated process that allows a cell to respond dynamically both to environmental stimuli and to its own changing needs.

This mechanism acts as both an "on/off" switch to control which genes are expressed in a cell as well as a "volume control" that increases or decreases the level of expression of particular genes as necessary.

So thats what DNA microarrays are used for.

To inderstand such a process, there is nothing better then animations...!

Here are some animation that i found very useful to fully understand Microarrays:

Note: The first animation is pretty simple and good for beginners:

Animation1

Animation2

Animation3

Any question, you're welcome.

Bioinformatics:Genomics:DNA Sequencing

Bioinformatics:Genomics:DNA Sequencing:

Bioinformatics lies in first place on DATA (Genomics & Proteomics...etc), so without data, Bioinformatics have nothing to analyse.

Before we can use analysis softwares we should have DNA or Protein sequences, so the first thing we have to do is sequencing.

The term DNA Sequencing refers to the methods applied to identify the order of DNA nucleotides or bases (Adenine, Guanine, Cytosine, Thymine).

Now with the advancements of technology, DNA Sequencing is indispensable for the most of biological researches because its the only way to provide almost complete and accurate data.

DNA Sequencing methods:
There are many ways or methods of DNA Sequencing but i like to introduce the sanger method explained by the beautiful and easy animation HERE


I picked the Sanger or (dideoxy) method, because its the more commonly used and the easier to apply.

Any questions comment.

Bioinformatics, Genomics

Bioinformatics, Genomics:

Genomics is the study of the entire genome of species (the sum of all genes of an organism) and their interaction with eachother, in contrast the study of a single gene is the role of molecular biology and genetics.
the study of genomes includes the DNA, RNA, Proteines levels.

recently there have been extensive sequencing projects of species genomes like the HGP (Human Genome Project) and a lot of other species (animals, insects, bacteria, viruses...etc).

You can find human genome sequences and many other species in the
UCSC Genome Browser
you'll find it a little complicated first but you'll get familiar with it very fast.

the UCSC Genome Browser contains now more than 45 complete genomes.

With the huge amount of sequences provided by sequencing projects, there is no way one can analyse it without the use of Bioinformatics tools, well thats good for us because if we have more than 3 billion pb that our brains will explode by reaching the 30 base!!!

Any questions or comments, you're welcome.