posts by vikram

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The motivation often comes from trying to google a question or topic only to find little-to-no answer. Should I have luck in answering it myself, I'll post it here with the hope that it helps other people with similar questions 🐢 back to Email GitHub

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Searching for sequences on GenBank - a few tips and tricks

This will be a “low-tech” post, i.e. one that doesn’t showcase code.

Over the past few years, I’ve done a lot of searches for genetic sequences on GenBank with the endgame of building phylogenetic trees. Here’s a list of things that have & haven’t worked for me when it has come to the task of finding specific genes for specific taxa.

A few good ways to set up the search term for nuclear genes are (ordered by specificity):

  • (Genus_species) NOT (whole genome) NOT predicted
  • (Genus_species) NOT (whole genome) NOT predicted NOT mitochondri*
  • (Genus_species) NOT (whole genome) NOT predicted NOT mitochondri* AND (gene1 OR gene2)

Note 1: I always avoid including sequences that have the word “predicted” in the title; I’d rather rely on sequences that have established identity. That said, including NOT predicted can be dangerous as the word “predicted” may appear e.g. in the title of the corresponding paper, but the sequence itself may be known with more certainity.

Note 2: For similar reasons, NOT (whole genome) may fare better than NOT genome

Note 3: OR needs to be nested within parenthetical statements. Taking the third bullet point as an example, a search without the the parentheses surrounding the OR statement such as (Genus_species) NOT (whole genome) NOT predicted NOT mitochondri* AND gene1 OR gene2 would amount to searching for (Genus_species) NOT (whole genome) NOT predicted NOT mitochondri* AND gene1 OR gene2. Therefore, all cases of gene2 for every species ever would appear in the search results!

Perhaps this list of notes will grow more someday, but that’s all for now


Written on June 13, 2020 by Vikram B. Baliga (vbaliga).