I was trying to find a plasmid origin of replication, ori-finder did not find it, and also I tried to blast against their database and try to align to other similar bacteria, but with no success.
Can someone recommend a fairly simple program for someone who is not a bioinformatician?
I was also looking into GC skew analysis, if someone can recommend a program for that as well, i would appriciate it.
Thanks.
Naama Geraffi
Try this, maybe you will find an answer
Hao Luo, Feng Gao, DoriC 10.0: an updated database of replication origins in prokaryotic genomes including chromosomes and plasmids, Nucleic Acids Research, Volume 47, Issue D1, 08 January 2019, Pages D74–D77, https://doi.org/10.1093/nar/gky1014
Dear Naama
I might help you regarding this, since i also work on plasmid biology. But before that i need to know the host of the plasmid that if it is a gram positive bacteria or a gram negative bacteria... Please let me know dat, den it wud help me precisely answer your query.
Dear Naama,
As the general protocol states, you initially anotate the plasmid sequence using rast or dfast, and identify the replication protein
After that using blastx program identify the closest homolog of the protein and understand the possible mechanism of replication of the plasmid.
Use tBlastn or tblastx program to identify the plasmid homolog that acquire same type of protein.
Go through the annotation and scrutinize the sequence for the probable ori in the plasmid homologs, if annotated
Search for the signature repetative sequences and boxes for tbe respective mode of replication .
Kazi Tawsif Ahmed
my plasmid's host is a gram negative bacteria.
i already did the annotation and i idetified the replication protein, I tried as I mentioned in my original post, to align the sequence to the ori sequences of other bacteria which were homologs, and still I could not find.
Abhijeet Singh
Hi, I already tried looking into the database. I tried the blast option and also manually with other homologous species to my bacteria's plasmid. unfortunately, I didn't find anything.
Dear Naama
Have you checked the replication protein in aclame database
Kazi Tawsif Ahmed
I entered the website now.
I tried to use the blast option but for some reason it says the input is invalid, even tough I just entered a simple amino acid sequence....
is there another option on that website I can check?
Naama geraffi you have toblast the sequence using the rep protein sequence in fasta format. The results will show the family of proteins to which ur rep protein belongs den u can have the idea of type of replicon. And the signature of ori sequence
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