Hello,
Can somebody tell me what is predicted protein and how one can retrieve all the predicted proteins of a particular organism? Thank you
•
written
by
mdfardin374 •
The predicted proteins are the output of a program that scans all possible coding sequences (CDS) (codon Start to Stop) in a genome and assigns a name and function based on matches with an experimental protein sequence database. To search, you need to find a program that fits your needs (prokaryotes or eukaryotes). If you just want to extract the CDSs from your genome, a simple biopython script can do that. But if you want to assign name and function (annotation), you need to use a program. I work with prokaryotes, the best program for me is Prokka.
I want to retrieve predicted protein (the protein that has no experimental evidence) already present in the database but I do not know how to retrieve it
for specific organism
If a genome page is available for this organism at NCBI then follow these directions (this is a random example genome).
Find predicted protein entries from the file.
$ zmore GCF_000209225.1_ASM20922v1_protein.faa.gz | grep "predicted"
XP_001623027.1 predicted protein [Nematostella vectensis] XP_001623028.1 predicted protein [Nematostella vectensis] XP_001623029.1 predicted protein [Nematostella vectensis] XP_001623030.1 predicted protein [Nematostella vectensis]
4. Extract the sequence for those ID's using faSomeRecords utility from Jim Kent at UCSC.
From which database do you want to extract these protein sequences ? In most databases you can search for CDS titled "Hypothetical Protein". These CDS are predicted sequences that show no homology to a known sequence.
Log in to answer this question.
Maybe this post helps C: Which software is suitable for protein prediction from whole eukaryotic genomes?
In combination with this website:
https://en.wikipedia.org/wiki/Gene_prediction
What do you suppose a "predicted protein" might be? Given that its name is an exact description of what it is.