Bioinformatics
So far I‘ve barely scratched the surface of the subject of applied bioinformatics. At first glance it feels quite overwhelming considering the amount of different computer tools, programs and databases available. I‘m sure the amounts of information one can retrieve from these would short-circuit any brain if they tried taking it in all at once.
Even so, little by little, pieces falls into place and one starts feeling excited about all the possibilities one discover in applied bioinformatics.
What it is
Bioinformatics is as the name suggests: computerized information about biology. More accurately defined it is “the application of statistics and computer science to the field of molecular biology”. The primary goal is to increase the understanding of biological processes.
Brilliant people are gathering all this information and make it into mind-numbing algorithms resulting in giant databases and computer programs. The applied bioinformatics is using these tools to solve theoretical and practical problems within molecular biology. This includes everything from finding genes, designing and discovering drugs, predicting how proteins interact to making models of the evolution. The most common application is mapping and analyzing DNA and protein sequences, compare different sequences and viewing 3-D models of the structures.
Tools
Most bioinformatics tools can be utilized worldwide, are available to everyone and can be applied in all kinds of research within the field. This again is brilliant because:
it shares all the knowledge worldwide
one gets access to information about the progress and research being done all around the world
it is a predictive tool to steer you in the right direction of a research project, which may save you a lot of time
one can see new possibilities in research projects that has met a “dead-end”
it can help you design a research project
...and so much more!
Source: Wikipedia - Bioinformatics
Examples of bioinformatics tools: |
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See also: |
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Subcellular Targeting Prediction Tools
By using these tools one can predict subcellular localization and this has become a valuable alternative to time-consuming experimental methods.
Here are some of these tools.The YLoc-database is the newest and uses natural language to explain why a prediction was made and which biological property of the protein was made reasonable for it.
By using these tools one can find motifs and pattern within the protein sequences. Motifs are also called the "fingerprints" of the sequence and are used to characterize a protein family and domains.
This tool allows the translation of a nucleotide (DNA/RNA) sequence to a protein sequence.
These two links are to were one can download phylogenetic analyses programs (free):
These sites are specialized biological databases that provides tools to identify and collect orthologous sequences
Phylogenetic trees can be presented in many ways. Branches can be scaled or unscaled, the tree can bee rooted or unrooted and it can have outgroups.
A denrogram is a broad term for the diagrammic representation of a phylogenetic tree
A caldrogram is a tree formed using cladistic methods. This type of three only represents a branching pattern, which means that the branch lengts do not represent time.
A phylogram is a tree that explicitly represents number of character changes through its branch lengths.
For more information: Wikipedia - Phylogenetic tree
Examples:
Phylogenetic tree of mammals
Phylogenetic tree containing extinct species
This class is only about the applied aspect of bioinformatics but we were given this homepage-assignment in order to get a better idea of what programming is and thereby an idea of what is behind all the bioinformatics tools we are using.
Therefore we learnt the programming language HTML. Computer science people might not even acknowledge HTML as a programming language at all, but by making a homepage from a blank document you are using only HTML data codes. It might be too easy for them, but for a beginner like me it was challenging enough!
Making a homepage is actually very fun and you can learn all you need to know online.
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