Dear,
I would like to categorise a large number of sequences (100-400 bp)
(about forty thousands) based on ontology (such as biological process,
molecular function, cellular component). Please, could you inform me
that which programme(s) in your website could be suitable for that?
Regards,
Or??un Ha??ar??z
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--
Sent via the guest posting facility at bioconductor.org.
Hi,
On Fri, Jan 31, 2014 at 9:16 AM, Or?un Ha?ar?z [guest]
<guest at="" bioconductor.org=""> wrote:
>
> Dear,
> I would like to categorise a large number of sequences (100-400 bp)
(about forty thousands) based on ontology (such as biological process,
molecular function, cellular component). Please, could you inform me
that which programme(s) in your website could be suitable for that?
Perhaps it is clear to others, but I'm not sure how one goes about
assigning function to a sequence in the absence of anything else?
Where are these sequences coming from?
Can you give more detail about what sort of sequences you are talking
about and what sorts of "functionality" you want to attribute to them?
And by what means it is valid to do so?
-steve
--
Steve Lianoglou
Computational Biologist
Genentech
Hi,
Please use reply-all to keep conversations on the bioc-list, that way
you can get better help and others can also use it as a resource.
That having been said:
On 31 Jan 2014, at 10:48, Orcun Hacariz wrote:
> Hi,
>
> These are the assembled sequences that were obtained from a
sequencing
> experiment. The sequences were annotated against different
databases
> using
> the blast programme. Basically, each sequence is matching a protein
or
> nucleotide in the public databases. But, I also want to annotate
these
> sequences based on their biological function (such as molecular
> function).
> For example, a sequence is matching with Cathepsin L1 protein. I
know
> this.
> But, I want to get the software blast this sequence against an
> ontology
> database and report the biological function(s) of this protein (it
> should
> report that this protein is associated with proteolitic activity,
for
> this
> example).
I think I'm still missing something.
You've used BLAST to associate the sequence to a particular gene. Now,
once you have the sequence <--> gene mapping, doing GO ontology stuff
on
the gene list is rather straightforward.
So, is your question how to do a GO analysis with *genes* using
bioconductor tools? Or do you want to have a Bioconductor tool that
you
can feed sequences to and have it match the organism and gene that
it's
coming from?
Or ... ?
-steve
--
Steve Lianoglou
Computational Biologist
Genentech
Hi,
My question is how to do a GO analysis with 'genes' using bioconductor
tools.
On Fri, Jan 31, 2014 at 10:04 PM, Steve Lianoglou
<lianoglou.steve@gene.com>wrote:
> Hi,
>
> Please use reply-all to keep conversations on the bioc-list, that
way you
> can get better help and others can also use it as a resource.
>
> That having been said:
>
>
> On 31 Jan 2014, at 10:48, Orcun Hacariz wrote:
>
> Hi,
>>
>> These are the assembled sequences that were obtained from a
sequencing
>> experiment. The sequences were annotated against different
databases
>> using
>> the blast programme. Basically, each sequence is matching a protein
or
>> nucleotide in the public databases. But, I also want to annotate
these
>> sequences based on their biological function (such as molecular
function).
>> For example, a sequence is matching with Cathepsin L1 protein. I
know
>> this.
>> But, I want to get the software blast this sequence against an
ontology
>> database and report the biological function(s) of this protein (it
should
>> report that this protein is associated with proteolitic activity,
for this
>> example).
>>
>
> I think I'm still missing something.
>
> You've used BLAST to associate the sequence to a particular gene.
Now,
> once you have the sequence <--> gene mapping, doing GO ontology
stuff on
> the gene list is rather straightforward.
>
> So, is your question how to do a GO analysis with *genes* using
> bioconductor tools? Or do you want to have a Bioconductor tool that
you can
> feed sequences to and have it match the organism and gene that it's
coming
> from?
>
> Or ... ?
>
>
> -steve
>
> --
> Steve Lianoglou
> Computational Biologist
> Genentech
>
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Hi,
On Fri, Jan 31, 2014 at 12:14 PM, Orcun Hacariz <orcunhacariz at="" gmail.com=""> wrote:
> Hi,
>
> My question is how to do a GO analysis with 'genes' using
bioconductor
> tools.
OK, in this case there are several packages that you can use to do
different types of GO analyses. You can browse the package available
in bioconductor here:
http://bioconductor.org/packages/release/BiocViews.html#___Software
To make it easier to do so, the bioc-folks have enabled packages to be
tagged by functionality.
There is a drill-down menu on the left hand side of the page you can
use to navigate these tags (aka "Views"). Dig down to:
Software > Annotation > GO
To filter packages that were annotated to work w/ gene ontologies.
You might try to start with either GOstats or goProflies.
Each package has one (or more) vignettes detailing how they are used
in an analysis, which should get you started.
HTH,
-steve
--
Steve Lianoglou
Computational Biologist
Genentech
Many thanks for the information.
On Fri, Jan 31, 2014 at 10:22 PM, Steve Lianoglou
<lianoglou.steve@gene.com>wrote:
> Hi,
>
> On Fri, Jan 31, 2014 at 12:14 PM, Orcun Hacariz
<orcunhacariz@gmail.com>
> wrote:
> > Hi,
> >
> > My question is how to do a GO analysis with 'genes' using
bioconductor
> > tools.
>
> OK, in this case there are several packages that you can use to do
> different types of GO analyses. You can browse the package available
> in bioconductor here:
>
> http://bioconductor.org/packages/release/BiocViews.html#___Software
>
> To make it easier to do so, the bioc-folks have enabled packages to
be
> tagged by functionality.
>
> There is a drill-down menu on the left hand side of the page you can
> use to navigate these tags (aka "Views"). Dig down to:
>
> Software > Annotation > GO
>
> To filter packages that were annotated to work w/ gene ontologies.
>
> You might try to start with either GOstats or goProflies.
>
> Each package has one (or more) vignettes detailing how they are used
> in an analysis, which should get you started.
>
> HTH,
> -steve
>
> --
> Steve Lianoglou
> Computational Biologist
> Genentech
>
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