Home
Reading
Searching
Subscribe
Sponsors
Statistics
Posting
Contact
Spam
Lists
Links
About
Hosting
Filtering
Features Download
Marketing
Archives
FAQ
Blog
 
Gmane
From: Jason Stajich <jason.stajich <at> gmail.com>
Subject: Re: remoteblast
Newsgroups: gmane.comp.lang.perl.bio.general
Date: Wednesday 14th May 2014 14:48:44 UTC (over 2 years ago)
So the BLAST services changed - not sure if we will still even support perl
based - it will require a developer tracking and testing to the new NCBI
resources since the have discontinued the older submission CGI resource.

You can run remote blast with commandline tool from NCBI as an alternative.

I think we will need to have a developer volunteer who wants to keep
working on tracking the webservices for NCBI to keep this module working.

Jason

Jason Stajich
[email protected]


On Thu, May 8, 2014 at 8:34 AM, Jolyon Holdstock
<[email protected]>wrote:

> Hi,
>
> I have a script that runs blast jobs against the databases at the NCBI.
>
> I use the  Bio::Tools::Run::RemoteBlast module for the blasting.
>
> It was working but is not now.
>
> The following is an example of the response I now get:
>
> --------------------- WARNING ---------------------
> MSG: req was POST http://www.ncbi.nlm.nih.gov/blast/Blast.cgi
> User-Agent: bioperl-Bio_Tools_Run_RemoteBlast/1.006901
> Content-Length: 788
> Content-Type: application/x-www-form-urlencoded
>
>
>
DATABASE=nr&QUERY=%3EHCV-54_contig_15+%0D%0ATCATAACAACCTTTTATGGTAAATACTAACAGCATGCCCATTTTACATGTGAGGAAACTGAGGCTTAGATCAGGTAAGTAGCTTATTCAGTGTTGCTCAAGTAAATACGTTTTAAGAACCCTCAGCCTCGCTCTCCTCTTCCTCAGGGCACACTTTTTTTTTTTTCCTTCCTACTGTGTGAGCTGTGGTGGGAATGTTAATCGGGATGCCTGTCTTTCCCTAGTCTTGGGGTCAGGCAAGTGCTCAAAGTCAGGATAAGCAAACTCTCCTTCCTGGGACTCTGAGGAAAGGCTCATTGATGGGGGAAATGGAGGGAGTGGATTCACTCCAGCTCAGCTCCGGGACAAGATGGCCATGGAGCTCCTGCTACATAAATGTCAGGGACTATCCTGGCTCCATCCTGCCTGCTTCCCTAGCTGCTGCCCAGCACTCACCTTATAAACATCCTTCGAGCTGGAGTTAGCCCGAATTGGTTTCTGTCCCTTGTGACCACTGAGCCCTGGCTGACACAATCACAGGCTGGCGAGCAGAGGTACCAGAC&COMPOSITION_BASED_STATISTICS=off&EXPECT=1e-10&SERVICE=plain&ALIGNMENTS=50&FORMAT_OBJECT=Alignment&CMD=Put&FILTER=L&HITLIST_SIZE=5&DESCRIPTIONS=100&FORMAT_TYPE=Text&ALIGNMENT_VIEW=Pairwise&PROGRAM=blastn
>
> 
> An Error Occurred
> 
> 

An Error Occurred

>

301 Moved Permanently

> > > > --------------------------------------------------- > > Can anyone suggest a fix? > > Thanks, > > Jolyon > > > Dr. Jolyon Holdstock, > Oxford Gene Technology > Begbroke Science Park > Begbroke Hill, Woodstock Road > Begbroke, Oxfordshire > OX5 1PF, UK > > T: +44 (0)1865 856852 > F: +44 (0)1865 848684 > E: [email protected] > W: www.ogt.com > > [cid:[email protected]] > > Oxford Gene Technology - The Molecular Genetics Company(tm) > > > * CytoSure(tm) arrays<http://www.ogt.com/clinical_genetics> - > Class-leading products and services offering the complete array solution > for clinical genetics research > * Cytocell(r) FISH probes<http://www.cytocell.com> - High-quality > products for the detection of gene rearrangements related to inherited > genetic disease and cancer > * Genefficiency(tm) genomic services< > http://www.ogt.com/genomic_services> - A tailored microarray and > sequencing service enabling high-throughput, high-quality genomic studies > for a variety of applications > > Oxford Gene Technology (Operations) Ltd. Registered in England No: > 03845432 Begbroke Science Park, Begbroke Hill, Woodstock Road, Begbroke, > Oxfordshire, OX5 1PF, UK > Confidentiality Notice: The contents of this email from the Oxford Gene > Technology Group of Companies are confidential and intended solely for the > person to whom it is addressed. It may contain privileged and confidential > information. If you are not the intended recipient you must not read, > copy, distribute, discuss or take any action in reliance on it. If you have > received this email in error please advise the sender so that we can > arrange for proper delivery. Then please delete the message from your > inbox. Thank you. > CytoSure(tm) and Genefficiency(tm) NGS browser: For Research Use Only; Not > for Use in Diagnostic Procedures< > http://www.ogt.co.uk/terms_conditions/trademarks_and_disclaimers> > > > _______________________________________________ > Bioperl-l mailing list > [email protected] > http://lists.open-bio.org/mailman/listinfo/bioperl-l >
 
CD: 3ms