[Biojava-dev] BioJava BLAST web services

[Scooter Willis]

I am planning on doing some testing of  a couple BLAST web services interfaces(assuming more than one exists) and see what they truly have in common and see how that would impact a BJ3 front end to multiple providers. My assumption is that they will be the same. I noticed on the NCBI Blast implementations the user was required to pass their email address as part of the web service call. They are concerned with abuse from external processes and they only allow one sequence per request. Same-Same but different is always fun!

>From wikipedia the following are listed as BLAST resources where more than one may offer a web service interface. Should BioJava3 try and support more than one?

Thanks

Scooter



Variations of BLAST


*	WU-BLAST <http://blast.wustl.edu/>  - the original gapping BLAST with statistics, developed and maintained by Warren Gish at Washington University in St. Louis <http://en.wikipedia.org/wiki/Washington_University_in_St._Louis> 
*	EBI's BLAST Services <http://www.ebi.ac.uk/Tools/blast>  - EBI's <http://en.wikipedia.org/wiki/European_Bioinformatics_Institute>  main blast services page.
*	FSA-BLAST <http://www.fsa-blast.org/>  - a new, faster but still accurate version of NCBI BLAST based on recently published algorithmic improvements
*	NBIC mpiBLAST <http://services.nbic.nl:4080/bb/cgi-bin/bb_login.cgi>  - at the Netherlands Bioinformatics Centre
*	Parallel BLAST <http://www-users.cs.umn.edu/~rangwala/final_bglBLAST.pdf>  - a dual scheduling BLAST tested on the Blue Gene/L
*	mpiBLAST <http://www.mpiblast.org/>  - open-source parallel BLAST
*	A/G BLAST <http://developer.apple.com/darwin/projects/blast/>  - implementation for PowerPC G4/G5 processors and Mac OS X, from Apple Computer <http://en.wikipedia.org/wiki/Apple_Computer> 's Advanced Computation Group <http://en.wikipedia.org/wiki/Advanced_Computation_Group>  and Genentech <http://en.wikipedia.org/wiki/Genentech> .
*	STRAP <http://3d-alignment.eu/>  - the protein workbench STRAP <http://www.charite.de/bioinf/strap/>  contains a comfortable BLAST front-end with a cache for BLAST results


[edit <http://en.wikipedia.org/w/index.php?title=BLAST&action=edit&section=13> ] Commercial versions


*	ThermoBLAST by DNA Software Inc. <http://dnasoftware.com/ThermoBLAST/tabid/110/Default.aspx>  - scans entire genomes quickly and accurately combing the power of BLAST with the most advanced thermodynamics parameters
*	PatternHunter <http://www.bioinformaticssolutions.com/products/ph/index.php>  - an alternative software which provides similar functionality to BLAST while claiming increased speed and sensitivity
*	KoriBlast <http://www.korilog.com/products>  - a reliable graphical environment dedicated to sequence data mining. KoriBlast combines Blast searches with advanced data management capabilities and a state-of-the-art graphical user interface.
*	microbial identification BLAST <http://www.sepsitest-blast.de/>  - a quality controlled database for in-vitro diagnostics. SepsiTest combines broad-range-PCR using ultra-pure reagents with Blast searches in a quality controlled environment.