I need to know the number of gene copies that encode an S-layer protein in certain bacteria whose genome is already annotated in NCBI
Also, how can I know whether some of them are truncated or not?
Some bioinformatic help pls... Thanks.
Just use the sequence of the gene of interest and blast it against the bacterial genome of interest to see if there are other homologs.
Once you have the different sequences (from the blast, as suggested by Michael J. Benedik: https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE=Proteins), you can aligne them with Clustal omega (https://www.ebi.ac.uk/Tools/msa/clustalo/) to see if some portions of you sequences are missing.
If you want to know the copy number of gene in bacteria you shuold use gene expression by using qPCR thats depend on you if like to use syber green or taq man method. If you have sequence for the target gene you can use NCBI Aliment by using blast
Just a small addition on the other people useful answers. When you perform your blast I would use tblastn to blast the protein you are interested in against the bacterial genome. Due to evolution you gene sequence may have been diverged and looking for the protein would give you more reliable results. Once you find the region where your protein return a hit you should also check for any stop codon interrupting the coding sequence or eventually some small intel that can cause a frameshift.
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