[DIYbio] Re: About bioinformatic, and fish eating starch

I'm thankful for the help I got here. I tried to play with BLAST,  I didn't change any algorithm parameters, and got both European Peach (Perca fluviatilis) and zander (Sander lucioperca) quite high on the "result list". Both carnivores (both raised in aquaculture). Don't know what to do with that fact. It's close to hybris for me to start this threat , and one thing in life is that id you have a good idea, other people might have had the same idea before you. So for the record here's an article that mentions the same thought I had. https://news.uci.edu/2020/02/19/veggie-loving-fish-could-be-the-new-white-meat/: "Heras, the paper's first author. 'However, most aquaculture fish are carnivores and can't handle plant lipids. Sequencing this genome has provided us a better understanding of what types of genes are necessary for breaking down plant material. If we scan additional fish genomes, we may find omnivorous fish with the right genes that could provide new candidates for sustainable aquaculture.'"

onsdag 22 mars 2023 kl. 02:59:12 UTC+1 skrev Sean Sullivan:

I've thought a bunch about how much of a time-saver it would be for scientists to have the sort of natural language search of scientific knowledge that you are describing (there are a few LLM-type attempts at this underway but that's a different topic), but as far as I know it's not that simple.

Here's a couple things you can try (not exhaustive, this isn't really my expertise):

1. BRENDA database entry for amylase (https://www.brenda-enzymes.org/enzyme.php?ecno=3.2.1.1) has a section "Select one or more organisms in this record" - see if some fish scientific names are in the list.

2. UNIPROT database entry for amylase cross-referenced by its Enzyme Commission number (https://www.uniprot.org/uniprotkb?query=ec:3.2.1.1) shows a list of organisms that have versions of the enzyme. A quick scan of the list shows at least one fish (Japanese Rice fish) in the list --> keep scrolling.

3. Take the DNA sequence of the amylase gene that you know and do a nucleotide blast search (Blastn - https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE=MegaBlast&PROGRAM=blastn&PAGE_TYPE=BlastSearch&BLAST_SPEC=). Paste the sequence in and search, it will pop up similar sequences it finds in different databases and will list the organisms the sequence came from.

These databases can be accessed programmatically via APIs if you know how to do that type of stuff. I hope you know lots of latin names...

Best,

Sean

On Friday, March 17, 2023 at 8:19:15 AM UTC-4 A. Ekergård wrote:

Writing as someone who couldn't finish a very short online course in bioinformatic and as someone working with aquaculture. If I read the fish monkeyface prickleback (monkeyface prickleback) can break down starch, I should be able to open a database like https://www.ncbi.nlm.nih.gov/ and find other fishes with the same genes for breaking down starch? Right? 

Hope I'm not looking too lazy for asking if anyone could help me? Hopefully it's not that complicated, but it's also not as easy as just writing: "what fishes produce amylase?"

Kind regards

Anders