So long SSAHA

nar databasesOne of the reasons we started this blog (and company) is because not only are the number of genomics databases, analysis tools and resources rising dramatically, they are in constant flux. New resources are born constantly (the graph on the right shows the rise in the number of resources listed in the annual NAR database issue), current resources are continually being updated and changed, resources merge (UniProt) and some just fade away.

I bring that up because Ensembl actually is not undergoing an update, having a major update and part of it is fading away… all at the same time. Ensembl undergoes a periodic update and was due for one in April, but they have postponed that update till July as per this Ensembl blog post. So, they are not undergoing an update.

But in July there will be several updates, Ensembl 50!, including an update to the web interface. We’ll keep you informed as to what the particulars of that update are and how the interface change might affect your usage of the site (and a review of course :).

Also, at the end of their post, the mention the demise of SSAHA which you are now able to access through the BlastView:

Last but not least, please note that from Release 50 we will no longer be providing the ‘ssaha’ sequence search. If you wish to run your own ‘ssaha’ sequence search you can download the files to generate the search hashes from our FTP site.

SSAHA, is a quick tool for sequence matching, as you can see from the Ensembl Help:

SSAHA (Sequence Search and Alignment by Hashing Algorithm)
SSAHA is a very fast tool for matching and aligning DNA sequences. It is most useful when you are looking for exact or ‘almost exact’ matches between two sequences. In Ensembl, you can use it to search against genome sequence assemblies.

So, I assume as of July it will be dead.

Of course, as they mention in the blog post, a similar search you can use for quick genomic sequence searches is the BLAT tool at the UCSC Genome Browser. Of course you could also download and install SSAHA yourself from the SSAHA homepage and obtain the hash tables from Ensembl’s FTP site.