Amino Acid Residues Changes/Mutation Causing Diseases

Question

[Thaman]

Hi Everyone,

I have been recently thinking to do some project of my own. I am getting more interested nowadays in bio-scripting and developing unique application with specific functionality. After brainstorming for long weeks I thought about one project, but dont know whether it's feasible or not. I dont have depth knowledge of moleculer level but idea is all I have got right now. Recently, in one lecture I heard about amino acid residues changes/mutation leads to diseases. For example, "Sickle cell anemia" an inherited blood disorder disease, where hemoblogin is defective. In normal Hemoglobin (Hb) where amino acid residue Glutamine is change into Valine at specific residues number.

My idea is finding all diseases which is caused by residues changes in specific amino acid chain (Polymer). I want to extract all information remotely or save locally in database for extending purpose.

Application Functionality/Approach

1. User will enter diseases like (sickle cell anemia) in search query

2. Result will be a. Normal sequence/gene and their name when it wasn't defective/mutated

   b. Two amino acid chain where one is normal and another is disorder/mutated

   c. Highlighting disordered/changed amino acids and number of amino acid.

   d. If possible displaying normal/defective structure of searched disorder diseases

   e. Letting user change amino acid residues in a chain and if instantly matches to any records in database then show disordered/mutated disease.

   f. Detail information about defective/mutated disease

   g. Link ID to other databases if available

   h. References

How can I find all genetic disorder diseases related due to change in amino acid? Which databases (NCBI, Swissprot, Uniprot, HGNC, OMIM) is best for my idea? Are there other databases where I can extract all disorder information at once so I can save them and identify residues changes? Are there already this kinds of project which functionality is same like mine?

At the same time, I am wondering whether my idea is feasible or not. To carry out this project what resources I have to go through or have prerequisite knowledge?

Thanks for your concern

Answer 1

[Pierre Lindenbaum]

A quick search in pubmed shows that it has already been done before for a restricted number of genes e.g.: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC29856

Something like SNPedia have also been used to store this kind of information Gene/Phenotype: see http://www.snpedia.com/index.php/Category:Uses_omim

See also this previous question on Biostar: Disease Associated Snps

Hope it helps
Pierre

Answer 2

[Tim]

For UniProt have a look at http://www.uniprot.org/docs/humsavar.txt. It'll make parsing a lot easier..

[Khader Shameer]

Tim, Thanks a lot for this.

[Thaman]

@Kim, it was really nice work

Answer 3

[Istvan Albert]

Try it out definitely.

The only note that I want to make is that in my opinion sickle cell anemia is the exception rather then the rule when it comes to associating diseases with mutations.

The way by which the mutation alters the oxygen carrying capacity of the haemoglobin is mechanistic (alters the shape) so it was easier to observe and correlate it to the mutated base. Most other diseases have far more subtle and distant actions that cannot be directly associated with the cause. So be ready to deal with less clear associations.

Don't take this as discouragement and please do try out your idea, and you can start with lookin at questions linked to by Pierre.

Answer 4

[Rm]

TinyGRAP database: a bioinformatics tool to mine G-protein-coupled receptor mutant data

It Attempts similar to what you are looking for.