Raw Bacterial Rna Sequence Db
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11.2 years ago
Iddo ▴ 230

Hi,

I am looking for a bacterial transcription database. GenExpDB seems to be mapped to known locus tags only. However, I am looking for raw sequence data, since I want to find mRNAs that are expressed from intergenic regions.

Thanks,

Iddo

EDIT: database should be downloadable.

rna expression bacteria • 3.4k views
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11.2 years ago
Josh Herr 5.8k

Since I work on environmental sequences I understand that most of the bacterial databases are skewed toward environmental markers. I had some luck with this bacterial transcript database (Bacterial Gene Expression Database: BGEdb) in looking for some rare transcripts, perhaps it will help you too. I'm not exactly clear on what you mean by raw sequence data, not sure if any datasets exist in the SRA, but hopefully this link works for you.

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11.2 years ago
Torst ▴ 980

Raw reads from high-throughput sequencing can be obtained from the NCBI Sequence Read Archive (SRA). It currently contains over 50,000 bacterial data sets. The majority are genomic DNA, but there is plenty of RNA-Seq to choose from.

Here is a link for the search term "bacteria RNA" which mostly gives you what you want: http://www.ncbi.nlm.nih.gov/sra?term=bacteria%20RNA

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