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Building a custom genomic database

Hello,

We generate in-house genome assemblies, annotation files for different microorganisms from time to time. I want to create a genomic database consisting of all the assemblies and annotations with the scope of adding future genomes. The database should be searchable to find specific genes, regions etc. I am thinking of creating a MySQL database, but then other users need to access MySQL and write commands to find out what they need. This is what I want to avoid.

Could anybody suggest any experiences of building custom genomic databases with an UI? Any tool recommendation would be great.

Thank you.

annotation database genome

MySQL database, but then other users need to access MySQL and write commands to find out what they need. This is what I want to avoid.

create a RDF-based database with a SPARQL endpoint and a few examples, just like uniprot: https://sparql.uniprot.org/sparql

2 answers

Tripal is a Drupal/PostgreSQL-based tool for building genomics databases with a UI you should definitely look into.

I recently came across this. I haven't tried it, but if you generate GFF files, then maybe it could be useful to you..

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