I have made few easy to understand tutorials for bioinformatics tools
So if you are a pure BIOLOGIST or a COMPUTER PROFESSIONAL or anybody who wants to learn about these basic tools -THIS IS THE PLACE TO BE.
I have tried my best to cover every detail on how to use these tools.As I have just started and not included many tools,so if anybody has any suggestions or want me include more
tools (if any specific ones), then mail me and I'll try my best to include it here.
I have chosen HUMAN DIHYDROFOLATE REDUCTASE (DHFR) PROTEIN for this tutorial.
Dihydrofolate reductases are ubiquitous enzymes which catalyze the reduction of folic acid into tetrahydrofolic acid. They can be inhibited by a number of antagonists such as trimethroprim and methotrexate which are used as antibacterial or anticancerous agents.
So what is so special about Dihydrofolate reductase:- DHFR is pharmacologicaly important intracellular target enzyme for a number of antifolate agents such as an anticancer
agent, antibacterial agent and antimalarial agent.
The basic question is -What you can do with this DHFR Protein with the help of bioinformatics
tools. Read further to find out!
GET AMINO ACID SEQUENCE
Sequence Retrieval:-First if you want to know about this protein , retrieve the amino acid or nucleotide sequence from databases.There is a huge collection of databases available online.To know about particular
databases, go to my Database section.
To know how to retrieve the sequence from the databases Click here
FIND SIMILAR SEQUENCES
Sequence Identity - Suppose if you want to check what are the other sequences which share
similarity with your sequence, then you can do this through online tools which are database dependent and tells about the
similarity of your sequence with other sequences. One assumes that through this you can infer the
homology (i.e., the sequences that share common ancestor)
One can infer Structural, Functional
and Evolutionary aspects through sequence similarity.
You can do sequence similarity through tools like
BLAST, FASTA. I have explained only BLAST in this tutorial as it is faster and more commonly used.
BLAST Don't go by the name, its not to explode you but yes it gives you so much information that too in such little
time, its incredibly good.
To sum up with BLAST is a sequence similarity search tool which compares your query sequence with the previously existing database sequences.
So explore BLAST with this tutorial .Happy BLASTING! Start BLAST tutorial
HOW ARE OTHER SEQUENCES IN THE SAME FAMILY RELATED TO EACH OTHER??
DHFR belongs to dihyrofolate reductase family. There
are many members in this family, so if you want to know how these sequences are related to each
other, Then go for MULTIPLE ALIGNMENT.
Multiple sequence alignment compares two or more sequence and it is done to find out relationship among sequences more importantly to find out evolutionary history i.e., to make a phylogenetic tree.
The tools for Multiple Sequence Alignment are:-Clustal W and
T-Coffee. I'll discuss Clustal W in detail.
Clustal W tutorial
WHAT ABOUT THE STRUCTURAL ASPECTS?
There are databases available which provide collection of structures of
proteins, One such database is Protein Data Bank(PDB). PDB deposits all the experimentally determined
structures. So one can explore the structure through PDB database to study the protein further in detail.
So start exploring PDB Tutorial
What happens if your protein does not have any structure in PDB ?
Protein Modelling is the best bet for that.
Protein modelling can be divided into four steps:
- Identify the proteins with known three-dimensional structures that are related to the target sequence
- Align the related three-dimensional structures with the target sequence and determine those structures that will be used as templates
- Construct a model for the target sequence based on its alignment with the template structure(s)
- Evaluate the model against a variety of criteria to determine if it is satisfactory
I'll explain Homology Modelling through Deep View/ SPDBV (Swiss PDB Viewer).
I assumed that SPDBV is already installed on your computer and you are aware of basic handling of the
tools. If not, then download SPDBV tool.
So what are you waiting for. Go ahead with SPDBV tutorial.
That's all from my side, so after these tutorials
you'll have a flavor of these tools and the more you play with these tools ,more you'll learn.
I will update this section with more tools like Phylogenetic studies by PHYLIP etc..
If you have any queries or suggestions then Contact me.