[protocols] Eel-pond/annotation questions

[Jessica Perry Hekman]

On 10/02/2014 06:18 AM, C. Titus Brown wrote:

> The problem here is that all of the commands expect a protein database, and
> BLAST treats DNA and protein databases quite differently.  (I'm also not sure
> the cutoffs or the scripts I've provided will work with DNA databases.)
> The easiest thing to do might be to grab the dog proteome, which should
> be available alongside the transcriptome somewhere -- at least, UCSC
> should make it available...

You'd think that would have occurred to me, but it didn't!

It was indeed right next to the dog transcriptome. I got it. formatdb 
was a little irritable about it:


[formatdb] WARNING: Sequence number 42467 
(gi|5835665|ref|NP_008483.1|CYTB_15041), 158 illegal characters were 
removed:
6 Es, 28 Fs, 38 Is, 58 Ls, 22 Ps, 6 Qs

(etc, for every sequence so far as I can tell). Something to worry about?

Anyways, I am re-running blastall now. Thank you.

Jessica