[mira_talk] Re: Assembly

  • From: Sven Klages <sir.svencelot@xxxxxxxxxxxxxx>
  • To: mira_talk@xxxxxxxxxxxxx
  • Date: Wed, 30 Sep 2009 15:16:53 +0200

I am not sure if I understood correctly, but NCBI always supplies the
sequences (when saving to file) as sequences.fasta/.gb/.whatever ..
This is just their default name.

hth,
Sven

2009/9/30 Sharmista Saha <sharmistasaha@xxxxxxxxxxxxxx>

> one more query, although it is silly, but I can't resist to ask, the gb
> file which I am downloading, is a particular gene file of a particular
> species, from the given link.
> http://www.ncbi.nlm.nih.gov/sites/gquery?itool=toolbar
>
> Although what I am saving is a seq.gb but,
> I think I may be wrong in that also ( may be it does not contain the whole
> database as required), can anyone suggest me what should be the correct one?
>
> Thanks and regards,
> Sharmistha
>
>
> On Wed, Sep 30, 2009 at 1:40 PM, Sharmista Saha <
> sharmistasaha@xxxxxxxxxxxxxx> wrote:
>
>> Thanks for all the help.
>> I will try your methods and get back to you.
>>
>> Regards,
>> Sharmistha
>>
>> On Wed, Sep 30, 2009 at 1:24 PM, Bastien Chevreux <bach@xxxxxxxxxxxx>wrote:
>>
>>> > Subject: [mira_talk] Re: Assembly
>>> > 3. I ran the respective command you provided, unfortunately, error
>>> says: bash: mira: command not found.
>>> > Now can it be easier for you to guide me to the root of my errors?
>>>
>>> You obviously did not install the mira executables in a system directory
>>> (/usr/local/bin comes to mind) or in a private directory which is in your
>>> PATH variable so that the shell can find it.
>>>
>>> Assuming you have no root priviledges and that you don't know how to
>>> extend the PATH environment for your current shell (bash), the easiest way
>>> would be to use the fully qualified name of the location where MIRA
>>> currently resides as command.
>>>
>>> So, if the executable is in the directory "/some/where/in/your/system",
>>> you need to prefix that directory to the mira command and things will run
>>> fine: "/some/where/in/your/system/mira"
>>>
>>> B.
>>>
>>> --
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>>>
>>
>>
>

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