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I have attempted a few searches for a list of origins of replication for plasmids in E. coli, but I was only able to find a list of origins, but not their individual sequences. The available plasmid maps are often extremely vague on where exactly do the origins start or end, and in any case it would be extremely tedious to collate a list of origins in order to determine the exact origin of replication of a plasmid.

Is there a database of origins of replication available anywhere that would allow one to perform BLAST searches on the plasmid sequence in order to obtain the compatability group of the plasmid, in cases where the plasmid's origin of replication is not specified?

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  • $\begingroup$ What do you mean by "unknown"? Is that naturally generated outside labs? Adgene shows positions of functional sequences and actual sequences. $\endgroup$
    – 243
    Jun 9, 2015 at 15:58

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Plasmapper Is quite good a recognizing common origins of replication. You will have to look up compatibility yourself. It is what I usually use when confronted with unnannotated plasmids.

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There must be some such information, because at the lab we are using the SnapGene software, and it is able to recognize the Ori sequences (and all other sequences). Since it is proprietary software, I doubt they would disclose their list, but others might have the same information.

If you really need to find your origin for your plasmid, you could try the demo. Good luck!

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Try this. I would suggest OriDB also, because it's precisely what you asked for. Getting the sequences out for easy blasting might be a chore, depending.

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  • $\begingroup$ OriDB is not what I asked for, since they don't have E. coli in their organism database. pombe.oridb.org/organisms.php $\endgroup$
    – March Ho
    Jun 9, 2015 at 19:04
  • $\begingroup$ That's why I didn't list it first. It appears to be the only database of Ori sequences, so it's a pity it is so small. $\endgroup$
    – Resonating
    Jun 9, 2015 at 19:06
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Go this URL And click pBR322 origin in the map. Then, the corresponding sequence will be highlighted.

2248-2867: pBR322_origin

2201 cccttaacgt gagttttcgt tccactgagc gtcagacccc gtagaaaaga 2250

2251 tcaaaggatc ttcttgagat cctttttttc tgcgcgtaat ctgctgcttg 2300

2301 caaacaaaaa aaccaccgct accagcggtg gtttgtttgc cggatcaaga 2350

2351 gctaccaact ctttttccga aggtaactgg cttcagcaga gcgcagatac 2400

2401 caaatactgt ccttctagtg tagccgtagt taggccacca cttcaagaac 2450

2451 tctgtagcac cgcctacata cctcgctctg ctaatcctgt taccagtggc 2500

2501 tgctgccagt ggcgataagt cgtgtcttac cgggttggac tcaagacgat 2550

2551 agttaccgga taaggcgcag cggtcgggct gaacgggggg ttcgtgcaca 2600

2601 cagcccagct tggagcgaac gacctacacc gaactgagat acctacagcg 2650

2651 tgagctatga gaaagcgcca cgcttcccga agggagaaag gcggacaggt 2700

2701 atccggtaag cggcagggtc ggaacaggag agcgcacgag ggagcttcca 2750

2751 gggggaaacg cctggtatct ttatagtcct gtcgggtttc gccacctctg 2800

2801 acttgagcgt cgatttttgt gatgctcgtc aggggggcgg agcctatgga 2850

2851 aaaacgccag caac

You can find various ori sequences from this site.

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  • $\begingroup$ I already know how to do this. I specifically stated that "and in any case it would be extremely tedious to collate a list of origins in order to determine the exact origin of replication of a plasmid. " and therefore asked if there was a database which solves this problem. $\endgroup$
    – March Ho
    Jun 10, 2015 at 4:16
  • $\begingroup$ It's just four or five in total, isn't it? pMB, modifiedpMB, R6K, p15A, pSC101, modified colE1. If you get a plasmid somebody constructed for recombinant DNA experiments, probably the ori is one of these. If you get plasmids from natural resources, you might not find complete match by alignment, but you could find a similar sequence among them. Or are there more types of ori out there? $\endgroup$
    – 243
    Jun 10, 2015 at 5:06
  • $\begingroup$ I mean once you get those 6 types of sequence, you can blast by yourself. You do not need to search plasmid from the URL I show. Did I miss something? $\endgroup$
    – 243
    Jun 10, 2015 at 7:04

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