Figuring out if a gene exists in a genome
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11 weeks ago
chronotope ▴ 10

Hey everyone! Quite a rookie question probably, but i wanted to ask this one for some time: how do you go about figuring out if a gene is present in a genome? My way of doing it was always: go to the genome annotation on NCBI / ctrl+F in the text for the name of the gene I am looking for. But it doesn't feel like the most efficient or even correct way, as sometimes automatic annotation either doesn't identify a gene, or annotates it falsely. I tried to find a way to BLAST a gene / a sequence against a given genome on NCBI, but I couldn't really find exactly what I was searching for. Maybe there is a bash tool / way to do this, preferably with display of sequence similarity scores / display of sequences for manual interpretation?

Cheers! a

gene genome blast • 369 views
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If you can't find what you're looking for in NCBI, you can check Ensembl and the UC Santa Cruz Genome Browser (specifically, the Table Browser tool).

Ensembl

UCSC Genome Browser

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I am moving this to a comment since this is a generic suggestion that does not consider that OP may be looking at sequences for organisms that are not in genome browsers. If OP finds this useful we can move it back to an answer.

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I'm so deep drowned in the world of microbes that I keep forgetting people also study "higher" species x) thanks for sharing, but indeed it's slightly irrelevant for me

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11 weeks ago
Shred ▴ 870

Blastx selecting a target organism gives exactly what you're looking for, starting from a cDNA sequence.

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