I’ve been a fan of ghostKOALA for a while, but uploading batches of 300mb files to a web interface was a pain. Enter kofamscan! KEGG published hmm profiles of each KEGG ortholog and implemented a tool to search amino acid sequences for them. There is still a web interface, but...
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Visualizing nucmer output
Download NCBI Protein Sequences
For a project I have been working on lately I wanted to download all archaeal gyrA sequences from NCBI and make a blast database out of them. I searched up and down the internet for a curl (or wget) solution, but didn’t find anything that did exactly what I wanted....
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