Can I reconstruct MAGs at time point 1 in my bioreactor and then check the presence/abundance of these MAGs at another time point in the same biorea?

We sequenced 20 samples of 2 different regions. A total of 40 samples. We used different primer pairs aiming to recover a broad range of groups. However, PCR/sequencing failed for different primers and samples. Now I don't have any sample sequenced with all primers. For a 12S I have 4 samples from one area and 20 from the other. I know it is far from ideal, but I can't re-sequence and wouldn't like to lose the produced data. It's the first baseline from areas in Amazon. I don't have any more ideas on how to compare the two areas with such a big sample number difference.

Can someone help me?

FASTA is best format for repersenting proteins but not suitable to repersent chemically modified peptides like terminal modifications, cyclisation, PTM, non-natural residues. Can you suggest best format.

Hi,

I have a protein sequence file (about 14.9 GB) in FASTA format. Each sequence has an ORF ID in the header line. I want to find the KEGG Orthology (KO) IDs that match these ORFs.

Can someone please suggest a tool or workflow that can handle large files and help me map ORF IDs to KO IDs?

Thanks in advance!

I was wondering whether there are any chemical or enzymatic methods to remove a single nucleotide from the end of DNA. Analogous to Edman degradation but instead of a terminal amino acid it removes a single nucleotide.

It could be either 3 or 5 prime end

It is fine if the nucleotide gets chemically modified, the ejected nucleotide is not of any concern.

The use of exonuclease might remove more than one base which can be a problem.

Hi all!

I want to construct a phylogenetic tree of all earthworm (Lumbricidae) COI sequences available on GenBank.

My search on the NCBI nucleotide database has retrieved about 10,000 sequences. Obviously, I can't construct a tree using all these. Also, I realize there will be redundant results, duplicates, and unverified sequences.

What would be my next step when dealing with these sequences? Should I clean my dataset of 10,000 sequences? If yes, how would I do that? Which tools or software are commonly recommended?

Any insight on the logical next steps would be immensely appreciated.

Greetings, everyone.

I'm currently optimising a protocol on eDNA extraction from freshwater samples for a species-specific assay. I want to test multiple workflows, including either filtration or centrifugation of water samples. (Both approaches have been previously shown to be reliable for the species of interest.) Here's the thing: for centrifugation, I plan to use at least 200 ml of water split into 50 ml falcon tubes. After centrifugation, the eDNA-containing pellets should be pooled into a single 1.5 ml microcentrifuge tube for DNA isolation. The thing is: how would you go about the pellet-pooling part? I've already tested it, and the best thing I've figured out is to carefully remove as much supernatant as possible and then gently aspirate the pellet into a large pipette tip. However, it feels somewhat unwieldy and I'm afraid this step may introduce unnecessary inconsistencies. If you have experience with this sort of pellet transfer and pooling, do you have any tips on how to get the best results possible?

(The already-published papers only mention that pellets were pooled, without additional specification. I plan to contact their authors to ask for details, but having some do's and don'ts from a larger number of people cannot hurt.)

I have a DMSO stock solution with a concentration of 0.1%. I want to dilute it again to a concentration of 0.05% which I will use in my cell culture media which I add with alfalfa plant extract with a concentration of 2.5%. how do I make the solution?

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