Create Database For Est Project
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11.4 years ago
Diogo Santos ▴ 20

Hello, I'm a BioInforamtic student finishing my master's thesis. I have assembly some 454 EST´s data, get blast and blast2go results for diferent datasets. I had to build a web site and a database to shown the results of that, but I can´t find a good way to do it. I had build an website with Joomla and I want my database to show there (probably I will use a wrapper). The problems is, wath to use for the database? I think of Jbrowse, but i dont´t know how to make it... It should have a "tablet view" of the contig, the blast results and the GO ontologies... And be possible to chosse diferent datasets to see diferent contigs...

database next-gen sequencing browser transcriptome • 3.0k views
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11.4 years ago

If you just have transcriptome data for that species, and you have produced a transcriptome assembly from the 454 reads, submitting them into NCBI SRA or EBI ENA as a Transcriptome Shotgun Assembly (TSA) dataset will make your data automatically accessible to the search services at NCBI and EBI. See for example the screen shot below from NCBI's Blast:

alt text

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thank you but my goal is create a website with the data available to everybody. I will try to had the view of the assembly (stats) and something like a tablet view for each contig. The blast result for each one and the GO classification for each one...

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11.4 years ago
Vitis ★ 2.5k

If you have a reference genome, Gbrowse (or the newer Jbrowse) would be a good choice to integrate all the information. It actually uses mysql as one of the backends so it's easy to implement your databases.

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Gbrowse has my first choise but i don´t have a referene genome...

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11.4 years ago
Gabriel ▴ 50

If you have knowledge of python (or any other object-oriented language), maybe you can use Django, a python web framework. It comes with an object-relational mapper in which you describe your database layout in Python code.

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I know some python and java (and perl and others...) but to be honest at first I can´t understand how can django help me... Because I need something to show the data to the user and i didn't know PHP to do it myself...

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11.4 years ago
Scott Cain ▴ 750

I suggest you take a look at Tripal:

http://tripal.sourceforge.net/

It is based on the PHP CMS Drupal, and uses Chado as the underlying biological database. There are several organism databases that are EST-only that use Tripal (they are listed on the Tripal homepage). There is an active community of developers and users for this project, and is part of GMOD. It provides several useful pieces:

  • Provides visualizations for chado "modules" such as features, analyses, libraries, stocks, and others.
  • Provides an interface for easy editing/updating of data in Chado.
  • Provides full text and categorical search capabilities for Chado content.
  • Can integrate GMOD tools such as CMap and GBrowse.
  • Integrates with powerful Drupal features like Drupal Views and Panels
  • Provides fully customizable PHP-based templates to allow for fine-grain control of the look-and-feel of the site.
  • Web-based management of Chado (i.e. installation of Chado v1.11 and loading of ontologies)
  • Loaders for GFF3 and FASTA format files.
  • Provides an API to allow for creation of custom extensions by anyone.
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I was actualy trying this, but I've encounter some problems in making it function... Do you know if it will work using xampp or sould I give up and start installing apache and mysql on my computer (of course the web site, when on line, will not function on xampp)

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Hi Diogo, Tripal and Chado will not work with xampp, as they require a PostgreSQL RDMS, and xampp uses MySQL.

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