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Functional interpretation of a bacterial transcriptome
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12 months ago
fhsantanna • 440
Brazil

I have results of differential expressed genes from a bacterial transcriptome generated through Deseq2.

The reference genome deposited in ENA (European Nucleotide Archive) is functionally annotated with GO terms.

Now I want to know if there is an specific functional category that is being activated in the test condition.

For this purpose, firstly I want to relate the locus_tag of the upregulated genes (I have a list of locus-tags) to the GO terms of the genome in embl file format.

Do you know a script that could perform this task? Or, at least a script that transform the embl file in a table that relates locus-tag and GO annotation.

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12 months ago
fhsantanna • 440
Brazil

I found a great tool for this purpose: Go retriever http://agbase.msstate.edu/cgi-bin/tools/goretriever_select.pl

It allows retrieving GO terms using as input Genbank acession numbers.

With these data I can utilize Bingo of Cytoscape for GO enrichment analysis.

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