[protocols] Eel-pond/annotation questions

[Jessica Perry Hekman]

That was it. Restarted blastall...

Jessica

On 10/2/14 11:12 AM, C. Titus Brown wrote:
> Hmm check to make sure -p T was spec
>
> ---
> C. Titus Brown, ctb at msu.edu
>
>> On Oct 2, 2014, at 11:57, Jessica Perry Hekman <hekman2 at illinois.edu> wrote:
>>
>>> 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
>>
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-- 
Jessica P. Hekman, DVM, MS
PhD student, University of Illinois, Urbana-Champaign
Animal Sciences / Genetics, Genomics, and Bioinformatics
https://www.impactstory.org/jphekman