Wednesday, April 23, 2014

Out of sequence

It's a car polish AND a software package!
I had occasion recently to use the venerable PatentIn software, which is thoughtfully provided by the USPTO for preparing sequence listings for patent applications.

It had been some years since I used PatentIn.  They're now on Release 3.5.1, which is an interesting coincidence, since it's been almost exactly 3.5 years since it was released.  

The manual for PatentIn includes a helpful "Version Control Log," which indicates that the software was originally prepared by Lockheed Martin (!) in 1998, although the first release did not come until 1999.  The software was updated twice in 1999, twice in 2000 and 2001, and then again in '03, twice in '04, in '06, in '07, and finally in '10.  Since then, nothing.

OK, so that might seem like they're updating this thing on a semi-regular basis.  But here's the thing: release 3.1 came out in January, 2001.  So the current release is based on 13-year-old software.  And it acts like it.  The interface is hopeless, the online help is unhelpful, and the end product is barely decipherable.

If the USPTO is going to require everyone to prepare sequence listings, you'd think that they could provide us something a bit friendlier to use.  At least commission an iPad app, for pete's sake.  How tough could it be?

But this got me to thinking:  is there really any reason for the sequence listing requirements to remain as they are?  I know that part of the original reason for the sequence requirements was to help the USPTO establish a sequence database that examiners could use for searching.  But that was a long time ago, before the entire scientific universe had been uploaded to the internet.  The reason I picked up PatentIn was a "Notice of Sequence Requirements" in a case, where the Examiner noted that a couple of short amino acid sequences in the specification did not appear in the sequence listing.  These were not claimed sequences.  They  are, in fact, sequences that appear in a scientific publication.  The publication is available on the web.  Why is  it still necessary for me to separately digest these for the USPTO?

Anyone? Bueller?  Bueller?




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