[Bioperl-l] Fwd: Changes to NCBI BLAST and E-utilities.

Mark A. Jensen maj at fortinbras.us
Fri Feb 5 11:32:12 EST 2010

all -- note too that blast+ has remote searches built in, and you can
access this functionality in StandAloneBlastPlus by specifying
-remote => 1 to the factory-- cheers MAJ
----- Original Message ----- 
From: "Chris Fields" <cjfields at illinois.edu>
To: "Mauricio Herrera Cuadra" <mauricio at open-bio.org>
Cc: "BioPerl List" <bioperl-l at lists.open-bio.org>
Sent: Friday, February 05, 2010 11:16 AM
Subject: Re: [Bioperl-l] Fwd: Changes to NCBI BLAST and E-utilities.

> Thanks Mauricio.  I think the only thing of impact will be the BLAST+ stuff 
> (and Mark has developed a wrapper for it).  We'll need to update the SearchIO 
> parser, so any BLAST+ output examples would be tremendously helpful.
> chris
> On Feb 5, 2010, at 9:48 AM, Mauricio Herrera Cuadra wrote:
>> Forwarding to the proper lists...
>> -------- Original Message --------
>> Subject: [O|B|F Helpdesk #889] Changes to NCBI BLAST and E-utilities.
>> Date: Fri, 5 Feb 2010 10:08:51 -0500
>> From: mcginnis via RT <support at helpdesk.open-bio.org>
>> Reply-To: support at helpdesk.open-bio.org
>> To: chris at bioteam.net, heikki at sanbi.ac.za, hlapp at gmx.net, jason at bioperl.org, 
>> mauricio at open-bio.org
>> Fri Feb 05 10:08:51 2010: Request 889 was acted upon.
>> Transaction: Ticket created by mcginnis at ncbi.nlm.nih.gov
>>       Queue: support at open-bio.org
>>     Subject: Changes to NCBI BLAST and E-utilities.
>>       Owner: Nobody
>>  Requestors: mcginnis at ncbi.nlm.nih.gov
>>      Status: new
>> Ticket <URL: https://helpdesk.open-bio.org/rt/Ticket/Display.html?id=889 >
>> Dear Colleague:
>> There are two changes I'd like to make you aware of.
>> As you may or may not have noticed, we have been working on a new C++ version 
>> of the BLAST binaries. In the coming months we will be moving the C++ 
>> binaries into prominence and (slowly) phasing out the C toolkit binaries.
>> There are many changes not least of which is a move to individual binaries 
>> for each program (blastn, blastp, etc).  We are not sure how many of your 
>> users use BioPerl with the BLAST binaries, my understanding is that many use 
>> BioPerl to to remote BLAST. However, there isa change to the BLAST results in 
>> Text and presumably HTML. This could have an effect on any parsers which 
>> scrape these formats and do not use XML. For obvious reason, we want to 
>> support only the XML format for parsing, but we thought we should give you 
>> heads up on this.
>> blast 2.2.22
>> Query: 3307 ------------------------------------------------------------ 3307
>> blast 2.2.22+
>> Query        ------------------------------------------------------------
>> A single line of gaps lacks the Query numbering in the blast+ output. The C 
>> version of blast has numbering in this case. Sample alignment shown below. 
>> According to users the blast+ output without the numbering breaks bioperl 
>> parsers. Wehave heard forma few but I think they may be older parsers?
>> The second issue is a policy concerning E-utilities. This was announced on 
>> the utilities-announce at ncbi.nlm.nih.gov mail-list but you may not have seen 
>> it.
>> As part of an ongoing effort to ensure efficient access to the Entrez 
>> Utilities (E-utilities) by all users, NCBI has decided to change the usage 
>> policy for the E-utilities effective June 1, 2010. Effective on June 1, 2010, 
>> all E-utility requests, either using standard URLs or SOAP, must contain 
>> non-null values for both the &tool and &email parameters. Any E-utility 
>> request made after June 1, 2010 that does not contain values for both 
>> parameters will return an error explaining that these parameters must be 
>> included in E-utility requests.
>> The value of the &tool parameter should be a URI-safe string that is the name 
>> of the software package, script or web page producing the E-utility request.
>> The value of the &email parameter should be a valid e-mail address for the 
>> appropriate contact person or group responsible for maintaining the tool 
>> producing the E-utility request.
>> NCBI uses these parameters to contact users whose use of the E-utilities 
>> violates the standard usage policies described 
>> athttp://eutils.ncbi.nlm.nih.gov/entrez/query/static/eutils_help.html#UserSystemRequirements. 
>> These usage policies are designed to prevent excessive requests from a small 
>> group of users from reducing or eliminating the wider community's access to 
>> the E-utilities. NCBI will attempt to contact a user at the e-mail address 
>> provided in the &email parameter prior to blocking access to the E-utilities.
>> NCBI realizes that this policy change will require many of our users to 
>> change their code. Based on past experience, we anticipate that most of our 
>> users should be able to make the necessary changes before the June 1, 2010 
>> deadline. If you have any concerns about making these changes by that date, 
>> or if you have any questions about these policies, please contact 
>> eutilities at ncbi.nlm.nih.gov.
>> Thank you for your understanding and cooperation in helping us continue to 
>> deliver a reliable and efficient web service.
>> I think you already adhere to this policy but should a user's script not meet 
>> these requirements, than the script will fail and requests will be turned 
>> away with an error message.
>> Scott D. McGinnis M.A.
>> 45 Center Drive, MSC 6511
>> Bldg 45, Room 4AN.44C
>> Bethesda, MD 20892
>> mcginnis at ncbi.nlm.nih.gov
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