Is PatScan RNA pattern searcher no longer available as an online webtool?
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4.5 years ago
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The PatScan pattern searcher is no longer available online.. Have they completely stopped maintaining the software as an online tool?

It used to be available through this address: http://www-unix.mcs.anl.gov/compbio/PatScan/HTML/scanner.html

But all is found at the moment is an installable Unix doppelgänger written in C: http://blog.theseed.org/servers/2010/07/scan-for-matches.html

N.B. I am mainly interested in the web version because my search must encompass the entire GenBank. Furthermore, I currently do not have the required computing resources to run a search using the offline version of the software.

DISCLAIMER: None of the answers here and none of the currently available motif search tools (be it web-based or command line-based) were of any use for my project. I was mainly interested in web-based tools for their efficiency as I had no access to good computing resources. Therefore I ended up buying an AWS Amazon account and scripted everything from scratch and wrote my own motif search programme jointly in R and command line. As a side note, if you are looking for conventional motifs RNABOB and RNAMOT should do just fine, but what I was looking was a very complex motif present on several RNA molecules and thus PatScan, RNABOB, RNAMOT, etc. were incapable of incorporating such requirements.

RNA PatScan RNA pattern • 1.5k views
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Maybe the time has come... the time that you'll have to learn how to use the command line...

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Yes I am very ignorant. Thanks for that!

Good luck! You'll probably need it very much!

I hope with your attitude someone is crazy enough to help you...

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It's perfectly possible that you don't agree with the statement of b.nota, but I don't believe it's necessary to strike out at him like you did here.

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I would also agree that this type of comment does not help the original poster and, in addition, it can come across as judgmental even if the author did not intended it to be so. Of course, at some point it does not matter who "started it" it is all about how to "solve it".

It does not take much to get opinions inflamed and have the situation spiral out of control - even though all participants are, what I believe very reasonable and overall positive individuals - once the question/answer becomes too personal we are all worse off.

I have undeleted this post mostly as a lesson to us all - how to recognize and avoid writing statements that can be easily misinterpreted and to think about how to de-escalate situations that seem to go awry.

That, in turn, is a very valuable skill to have - especially for bioinformaticians - and other people working jobs where they rely too much on computers whose feelings won't quite get hurt...

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What ever, I think I am gonna try stack overflow for while, and downvote rethorical questions such as these there. Will save a lot of my ignorant time.

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I think what you will find is that "punishment" does not work. It is an illusion that downvoting somehow makes things better. It only makes everyone more miserable and sadder - including the person doing the downvoting. Based on my own personal observations people that like to downvote are less happy and positive towards life than those that do.

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It's not about punishment, it's more a matter of removing rotten apples. That's my ignorant opinion.

If OP can't take good advice (learn scripting), don't come here spoiling it for the rest.

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We value your contributions to this forum, but keep in mind we like to keep the bar as low as possible for new users.

With regard to "learn to script" that's "the answer OP deserves but not the one OP needs right now". It's, in essence, good advice but quite a big hurdle for someone just starting.

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Sad to hear you are still in your mantrum. Good luck with your research endeavors, hope you find a solution for your problem(s) soon.

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4.5 years ago

While I don't know of online tools there are several command line tools that may be viable alternatives such as:

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FuzzNuc can be used via a web interface here and here.

' : In general you are going to be at the mercy of the web sites in terms of what you can do. Searching entire genbank via a web interface is a tall order but it seems like the Argonne lab site allowed you to do that in the past.

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