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Recommended data warehouse tools for bioinformatics search?

I'm a bioinformatician with some Perl programming skills. However other members in my lab didn't know much about bioinformatics. Sometimes they need to search for some specific gene IDs and obtain their sequences, structures (GFF) and GO annations. As the organisms are non-model species, public servers such as Ensembl or Phytozome are not sufficient. I want to do a web interface with simple data search function and using SQL database as backends. I tried building local InterMine server but it was too complex. Any other good open source tools?

genome gene sequence
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updated by Jean-Karim Heriche Jean-Karim Heriche • written by billzt • billzt

3 answers

Unless you need something really extraordinary in terms of presenting the genomic data, abandon the idea of writing such system from scratch, especially as a first step. Use Jbrowse, collect opinions, and if end users really need more, then rather invest your time into installing a local copy if ENSEMBL than reproduce maybe 30% of functionality in X weeks. And give the users/institute hard to maintain, one in a world solution, which will die once you change the job.
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written by Darked89 Darked89

All the data had been stored on local server, in FASTA, GFF, or tab delimited files. They could be dumped into databases. We want to implement data search frontends like the "key word search" and "gene page" of Phytozome or Metazome.

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written by billzt • billzt

See if genoverse fits your needs. It doesn't need any database back-end and can work with many file formats. Otherwise, you could turn tab-delimited files into SQLite tables and write simple cgi scripts to access the data.

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written by Jean-Karim Heriche Jean-Karim Heriche

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