Build a candida genome database

Question

[ibm2012001]

Hi All,

I am new to the field of bioinformatics and currently I am pursuing my Masters in it. I have taken up a project of creating a candida genome database and incorporating few bioinfo tools in it like BLAST, primer search etc. I did check out some of the already available candida genome database, but mostly all of them cover only few species. I want to create a comprehensive database. Please tell me how should I start and what all things I need to learn to make this database. I am completely new to bioinformatics and have no knowledge of how to build databases.

Thanks in advance.

Answer 1

[lakhujanivijay]

Since, you're completely new to bioinformatics and have no knowledge of how to build databases; stop for a while and think:

Why to take up a project which requires building a database? Is it something that your project guide/ mentor told you to do or you really want to make a database?

How will your database will add value to the already existing database (or it will just add all the possible Candida strains)? Will it really be useful to public or will it exist as a closed MSc. project in some random CD/ folder forever lost in the eternity?

Why a database for Candida and not any other organism? Remember there are thousands of databases and databases of databases like the galaxies in the universe. Would you really like to add yours in that list?

I am not trying to discourage you in any way. This is important to think about as you will be putting in your precious time and efforts to turn your idea into reality.

If you have solid answers to above questions, go for it.

[ibm2012001]

This project was suggested to me by my project guide and the reason why we chose candida was because candida is an emerging and a very important pathogen. Also genetic modifications keep happening in candida as it can adapt itself in any environment therefore a platform is needed wherein maximum candida species are present alongwith their genomic and nucleotide information.

I wanted to work on a software based project specially related to database and web development.Since I am not from a biology background I have to work a lot on my concepts too. I don't think I'll be able to create a database like CGD in 6 months.Earlier CGD (candida genome database) focussed only on candida albicans and slowly they have started adding other candida species too. Now they have included 4 species. Most of the already existing databases focus only on albicans therefore I wanted to make a more comprehensive database including other candida species that are emerging as an important pathogen. I was asked to do a classification all the candida species that I have found into pathogenic, non pathogenic and opportunistic species which is not available in any of the already existing candida database.

I cannot change the topic for my project now as it has been submitted already to the HOD. So how should I proceed now? How should I create something simple but different which will be useful for the research community? I am too lost right now.

Answer 2

[Persistent LABS]

Whats your purpose of creating the database. Do you want to create the local sequence database of candida genome? Then creating a local blast database would be sufficient. Please clearly state why you want to create the db.

[ibm2012001]

The reason behind creating a database for candida is that phylogeny of candida keeps changing as candida adapts itself to any environment. Like earlier candida albicans were not opportunistic but now they have emerged as an opportunistic pathogen. Similarly many such candida species who were earlier non pathogenic have emerged as pathogenic now. Most of the candida database that already exist focus mainly on candida albicans therefore I want to make a more comprehensive database which will include various other candida species who are also important. This database will help the research community who are interested in the microbiology of candida as they will get all the genomic and nucleotide information of most of the candida species on one platform and with the help of some tools they can analyse the data too.

Will creating a local blast database be sufficient for a masters thesis?

[Persistent LABS]

There can be many possible things that can be done, depending on available data.

1. First of all create a list of all Candida species and see whether you can classify them w.r.t their pathogenic nature (pathogenic, non pathogenic and opportunistic), based on either literature survey or from any preexisting database.

2. Are there any marker genes that can be used to classify them ? If so, then you can collect the gene/protein sequences from each candida strain and build a phylogeny/HMM-based/PSSM based models. So when a new sequence emerge, you can use the model to predict whether the new strain can be pathogenic, non pathogenic and opportunistic.

I would suggest that better to further narrow down your objective so that first you solve one problem and then expand on it.

Thanks

Persistent LABS