[mira_talk] Re: Fishy tag

pfouahahaha, I didn't even notice!

So sorry for this, I usually always choose to add the sequence, I must
have been distracted.

Louis

________________________________________
From: mira_talk-bounce@xxxxxxxxxxxxx [mira_talk-bounce@xxxxxxxxxxxxx] On Behalf 
Of Bastien Chevreux [bach@xxxxxxxxxxxx]
Sent: Wednesday, February 16, 2011 4:49 PM
To: mira_talk@xxxxxxxxxxxxx
Subject: [mira_talk] Re: Fishy tag

On Wednesday 16 February 2011 22:04:59 Louis Letourneau wrote:
> I attached the file.

You downloaded a GenBank file without the sequence :-)

Here's the tail of your file:

----------------->8   snip   8<--------------------------
                     /protein_id="YP_495282.1"
                     /db_xref="GI:87161775"
                     /db_xref="GeneID:3913629"
ORIGIN
//
----------------->8   snap   8<--------------------------

The same file with the sequence should look like this:

----------------->8   snip   8<--------------------------
                     /protein_id="YP_495282.1"
                     /db_xref="GI:87161775"
                     /db_xref="GeneID:3913629"
ORIGIN
        1 actactgctc aattttttta cttttatcga ttaaagatag aaatacacga tgcgagcaat
       61 caaatttcat aacatcacca tgagtttggt ccgaagcatg agtgtttaca atgttcgaac
      121 accttataca gttcttatac atactttata aattatttcc caaactgttt tgatacactc
----------------->8   snap   8<--------------------------

and end like this:

----------------->8   snip   8<--------------------------
  2872681 tctcgtatta gctcattgat tatctagtca taattcaagc aactactaca atataacaaa
  2872741 atcctattta taacgcaagt tcattttat
//
----------------->8   snap   8<--------------------------


Make sure to tell NCBI to add the sequence and also to choose "GenBank(full)"
as format when using the "Send" functionality there.

I'll see whether I can catch this kind of errors a bit earlier in the reading
process of a GenBank file and give a better error message.

B.

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