I'm new to the field of metatranscriptomics and currently using a software for differential expression of a control vs treatment experiment. I need to use an annotated genome of E. coli Nissle (one of the many genomes I will analyze in the future) and will need to import these sequences for the analysis but I'm not sure where I can download it from. Currently, I'm using a genome assembly from NCBI but this is not annotated. Annotation using the software (Geneious Prime) only provides me with common gene annotations (polyArg, PKA site, etc.).
Many thanks for your inputs!
Hi Ryan:
If you are also planning to work with livestock species, perhaps you can use GALLO (https://academic.oup.com/gigascience/article/9/12/giaa149/6055471) after downloading the genome assembly from NCBI.
Anyway, I believe these materials are also useful to you:
https://molbiol-tools.ca/Genomics.htm
I hope it helps.
BioCyc and EcoCyc are very good reference databases if you are going to work with E. coli genomes. The entire annotation should however also be available via NCBI, eg. for the Nissle 1917 strain https://www.ncbi.nlm.nih.gov/nuccore/NZ_CP007799.
Make sure that you have selected "GenBank (full)" as format when downloading the annotations file via the "Send to" menu.
You can search on NCBI Geo if you find the transcriptomics dataset you need you can check out the article in which it was published. Some of the papers have annotated data provided as supplementary
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