why do I give a dog genome sequence and it gives me nothing about dogs?
1 answer
Worth splitting "nothing about dogs" into two cases, because the causes are completely different.
If you got zero hits at all, the query most likely wasn't parsed as DNA - a FASTQ pasted where FASTA was expected, quality or numbering lines mixed in, or a whole genome pasted into web BLAST, which caps the query size.
If you did get hits but they're human, mouse, cow and so on, that's normal and nothing is broken. BLAST ranks by alignment score, not by how well the organism matches what you expected, so a conserved region will put other mammals above the dog. Put Canis lupus familiaris (taxid 9615) in the Organism field and re-run - if dog hits show up then, the search was fine all along and you were just reading the top of the list.
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some more information might help to receive meaningful answers. If not, we're just as well random guessing
you're using the wrong database for instance?
BLAST can be run a lot of ways in a lot of places. Underlying BLAST in all its forms is the BLAST software. It needs several things to work and you can get an idea of what those are by working through these Jupyter Notebooks you can get in temporary, anonymous remote sessions right in your browser without logging in or anything by going here to my blast-binder repository and clicking '
launch binder'. badge you see there.After the session spins up, (this may require some patience the first time depending where you are in the world right now, if it needs to build the image), you can work through the first three available notebooks, starting with the first one listed at the top. Indeed, these comments and that first Jupyter
.ipynbfile is likely the only one you need to work through to understand why lieven.sterck is pointing out that what you have provided doesn't help us help you. The intro stuff about the Jupyter UI may be a little outdated though so overlook that; importantly, I just tested the four Jupyter Notebooks and they run still (although you may need to try in a few different sessions as the MyBinder service can be taxed easily). You can just use the top menu to do 'Run' > 'Run All Cells' to run an entire notebook. After it works with the test stuff you may be able to even start to plug in some of your data. Although the limited computational resources offered by the Jupyter Community-supported MyBinder-service may not be enough for an entire metazoan genome. So you may want to play around with plugging in pieces and you may need additional resources you know of from the canine molecular biology domain to try and get something working.