Bioinformatics exercise on extracting FASTA sequences corresponding to taxon from a microbiome sequencing experimet in another file (.TSV)

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3.3 years ago

flisosergio • 0

Please see attached taxonomy_metadata.tsv (tab-delimited) and sequences.fasta files.

https://anonfiles.com/N0W39188pd/Assignment_zip

These are output files from the tool QIIME2 (for further details, please see https://docs.qiime2.org).

What would be an easy/short script to extract sequences that correspond, for example, to taxon k__Fungi;p__unidentified;c__unidentified;o__unidentified;f__unidentified;g__unidentified;s__unidentified? then run the sequences through BLAST to get the results. Please attach your results and source code

I tried using python and pandas packages but... I don't really have knowledge in programming and I'm quite lost bc of the file types and how they are structured. I don't think working with them as tables will give an easy answer.

Thanks for your help!

fasta homework • 758 views

ADD COMMENT • link updated 13 months ago by Ram 43k • written 3.3 years ago by flisosergio • 0

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That's a really bad title. Please read this: https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1002202

Using a proper title is critical to people taking the time to even read your post.

ADD REPLY • link 3.3 years ago by Ram 43k

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