Sorry for all the "building FASTAs and genomes from proteomics and nextgen stuff" posts. If your organism is all annotated and clonal this is probably boring." However, if you are studying something that hasn't been perfectly annotated or has individual genetic variation this is a great time for you! So many options!
InterPro isn't new, by any means, but InterProScan (scan is the web portal) was just upgraded last week and EMBL-EBI has some very convincing arguments (like near the end of this YouTube video) for why you should be using it for your annotations.
Okay -- having a gorgeous web interface shouldn't be the reason to use something -- but when it's backed with this kind of ridiculous power, it doesn't hurt. All these databases feed in seamlessly and you can choose to use some or all of them.
Like the pBLAST web interface you can only search one thing at a time, which is great if you're down to a small list of quantitatively interesting things. However, there is a stand-alone program (InterPro, I think). It can only be installed in 64-bit Linux, so no casual Windows people.
Okay -- but the reason I've been running InterProScan is actually because of something else from EMBL -- it's called UniFire and there isn't tons out on it yet.
However, there IS a free class on Wednesday July 10th on UniFire. You can register for it here.
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