The BioPerl 1.6 stable release is now available. It contains HIVQuery modules and many, many other goodies. Visit the release page

Your feedback is very important. As always, contact us with bug reports and enhancement suggestions.
MAJ 25 Jan 2009

hivq.PL has been updated. The distribution options now include a Windows executable, containing everything necessary to run HIVQuery without a separate Perl interpreter.

Significant bug fixes have also been made on the underlying module Bio::DB::Query::HIVQuery; in particular, problems with retrieving annotations have been fixed. These changes have been committed to the BioPerl trunk, called bioperl-live.

Your feedback is very important. As always, contact us with bug reports and enhancement suggestions.
MAJ 28 Jan 2009

A sequence query tutorial is now available. It briefly describes the idea of querying databases, and gives details and examples for writing HIVQuery-style queries. Thanks to colleagues in The Netherlands for the suggestion!

Your feedback is very important. As always, contact us with bug reports and enhancement suggestions.
MAJ 30 Jan 2009

The web-based interface to HIVQuery seems to be working well as of the time of this post. The ISP, Network Solutions, has been working behind the scenes; many thanks to them. Fixes in annotation slurping are working as well. Enjoy-

Your feedback is very important. As always, contact us with bug reports and enhancement suggestions.
MAJ 01 Feb 2009

The HIV coreceptor predictor has been updated with new features. It can now handle degenerate nucleotide sequences (those containing IUPAC ambiguity symbols). The tool will automatically analyze all possible unamibiguous amino-acid sequences implied by the ambiguities present in the input sequences. Each amino acid sequence is displayed and scored; the average score (and prediction for that average) over all possible combinations is also reported. Many thanks to a French colleague for this valuable suggestion.

The V3 loop search options have also been rationalized, and a bug or two fixed. For an overview of the new features, see the the preprocessing help page.

Your feedback is very important. As always, contact us with bug reports and enhancement suggestions.
MAJ 03 Feb 2009

Recently on EVOLDIR, Gavin Gouws at the South African Institute for Aquatic Biodiversity put out a distress call regarding an old phylogenetic analysis program, BIOSYS2. This program, in FORTRAN, was apparently the ancestor of PAUP. I tweaked the source, fixed some bugs, and increased the array dimensions to work with modern datasets. A Windows stand-alone executable, compiled with GNU FORTRAN under Cygwin, is available here.

Your feedback is very important. As always, contact us with bug reports and enhancement suggestions.
MAJ 05 Feb 2009

The HIV coreceptor predictor has been updated. When expanding degenerate sequences (sequences containing ambiguity symbols), there is now an option for reporting just the average score over all sequences in the expansion, without returning each disambiguated sequence separately. Returning the average only is a comparatively fast calculation, so the program will analyze sequences representing up to 16384 combinations. The option to return and score each combination separately is still available, with the previous limit of 512 combinations. See the updated help page for more details. Other efficiencies have been added and minor bugs fixed.

Your feedback is very important. As always, contact us with bug reports and enhancement suggestions.
MAJ 27 Feb 2009

The HIV coreceptor predictor now allows the use of the improved cutoff scores described in Poveda, Seclén, González, et al 2009. These cutoffs were shown to improve predictor performance with respect to virus phenotypes emerging under Maraviroc therapy in the ALLEGRO trial. Please cite this paper if you publish results using this predictor.

Your feedback is very important. As always, contact us with bug reports and enhancement suggestions.
MAJ 24 Mar 2009

HIVQuery has been updated with new options for data retrieval.

Besides FASTA formatted sequences and annotations, users can now retrieve annotations in XML, valid against http://fortinbras.us/HIVDBSchema/1.0. This is a set of XML Schema definitions designed by Fortinbras that represent the underlying structure of the Los Alamos HIV Sequence Database. The .xsd files can be obtained directly from the HIVDBSchema/1.0 URL.

Sequence data can also now be obtained in NeXML format, an emerging XML standard for evolutionary data exchange. Details on NeXML can be obtained at http://www.nexml.org, and extensive technical discussion is available at NESCent's EvoInfo Working Group wiki.

There has been a rationalization of the query interface. A single button runs a query. Following the run, the user is presented with data download options.

Please notify me of any issues that arise with these experimental features.

Your feedback is very important. As always, contact us with bug reports and enhancement suggestions.
MAJ 11 Apr 2009

bioperl-max is a 32-bit Ubuntu Hardy(8.04)-based Amazon Machine Image (AMI), fully loaded with the BioPerl production packages (bioperl-live, bioperl-db/biosql, and bioperl-run), along with a large variety of open-source bioinformatics tools. The tools include popular apps like blast, hmmer, and HyPhy, as well as R and the GNU compiler suite. Fortinbras maintains this AMI as a free service to the research community. Check out Amazon Web Services to get started in the cloud.

Your feedback is very important. As always, contact us with bug reports and enhancement suggestions.
MAJ 10 Jun 2009

We've added a page containing links to Fortinbras resources beyond the public applications. Please have a look.

Your feedback is very important. As always, contact us with bug reports and enhancement suggestions.
MAJ 11 Jun 2009

bioperl-max, v0.1.1 is available, with Amazon Machine Image id ami-b55dbbdc. Newly installed are a git clone of perl6 (Rakudo) and svn revision r39729 of parrot. NeXML is updated to r1136, and bioperl-live to r15800. Fortinbras maintains this AMI as a free service to the research community. Check out Amazon Web Services to get started in the cloud. Happy coding!

Your feedback is very important. As always, contact us with bug reports and enhancement suggestions.
MAJ 23 Jun 2009

A gene filtering and clipping feature has been added to HIVQuery. This has been implemented as a post-processing step after the initial query has been run, when the user makes download format selections. Details can be found on the help page. Many thanks to David Posada for this suggestion.

Your feedback is very important. As always, contact us with bug reports and enhancement suggestions.
MAJ 09 Aug 2009

The spaTyper repeat and spa database has been completely updated. 329 repeat sequences and 5719 known spa types are now recognized. I appreciate the use spaTyper has been getting in recent weeks. If you find it useful, please tell your colleagues, and let me know how I can improve it.

Your feedback is very important. As always, contact us with bug reports and enhancement suggestions.
MAJ 20 Sep 2009

bioperl-max, v0.1.2 is available, with Amazon Machine Image id ami-1ad03273. Newly installed are the short-read assembly tools bwa, maq, and samtools. Bioperl packages bioperl-live and bioperl-run are updated to r16427, and contain maq, bwa, and samtools support. Fortinbras maintains this AMI as a free service to the research community. Check out Amazon Web Services to get started in the cloud. Happy coding!

Your feedback is very important. As always, contact us with bug reports and enhancement suggestions.
MAJ 28 Nov 2009

I've fixed a major bug that was resulting in different score averages for degenerate sequences depending on whether "Average score" or "Full expansion" was selected. The scores are now the same and correct for both selections. A sequence type selector has also been added: when too many ambiguities are present in a nucleotide sequence, the code can wrongly interpret the sequence as "amino acid". The control forces the selected interpretation regardless of the residues present in the sequence.

I apologize for any inconvenience these bugs may have caused users.

Many thanks to the group at U. Roma "Tor Vergata" for catching this bug, and sending test data to work it out.

Your feedback is very important. As always, contact us with bug reports and enhancement suggestions.
MAJ 03 Dec 2009

The FSSM coreceptor predictor is now available as a SOAP-style webservice. An easy object-oriented Perl interface to this service, FSSM::SOAPClient, can be downloaded and installed via CPAN. The web service description can be found at http://www.fortinbras.us/soap/fssm/1.0. More details here. Happy Coding!

Your feedback is very important. As always, contact us with bug reports and enhancement suggestions.
MAJ 21 Jan 2010