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Hello.
I would like to share with you a quick tour on EMBOSS a nice
tool, a suite of tools, that could be a one stop shop for
most of your basic bioinformatics analysis.
If you have any question about bioinformatics, can I do this?
Can I do that?
I want to set a primer.
I want search a motif.
I want to do some alignment, basic alignment.
I want to visualize the structure, 2D
structure, 3D structure.
I want to cut a sequence, paste a
sequence, or reform a sequence.
I want to do restriction enzyme [INAUDIBLE].
I want to design the primer, and so many different things.
If you have any questions, basic question, one the first
places you can go look for an appropriate tool, is EMBOSS.
There are a number of different tools out there,
individual scattered tools around the world, around the
globe, on the internet.
But EMBOSS has been there for a long, long time, and it's a
very good, stable collection of tools, basic tools.
So how do we start?
Like I said, there are different places where EMBOSS
servers are hosted.
It's an open source project.
You can download and install and run your own version of
EMBOSS if you want.
But if you're looking for a quick solution, quick
analysis, a simple analysis, then there are a number of
EMBOSS servers that are public servers that are
available out there.
So I would always search like this.
EMBOSS, go to Google, EMBOSS, web server.
So if you search for that, you're going to get this link.
The first link gives some of the popular servers that are
already listed in the EMBOSS original project page.
So you click on the EMBOSS servers, and you scroll down.
So these are some of the EMBOSS servers which are based
on EMBOSS explorer.
I want to quickly show you two options, two servers
that are out there.
The first one is from Netherlands.
So if you just click on that.
So this is EMBOSS, all these different tools that you see
here, this menu that I'm scrolling down.
These are different tools that are used for several different
things in a regular biology stuff.
So I go back.
And if you wanted to use a tool, a server from an
American institute, here is Purdue University's server.
So you click on that.
You will end up in Purdue University's EMBOSS server.
And like I mentioned, EMBOSS is a collection of a huge
number of routinely used simple analysis tools.
As you see, you can start with alignment.
You could do dot plots.
You could do local alignment, global alignment.
You could do multiple alignments,
using popular programs.
You could generate nice graphic
displays, pretty plots.
You could edit sequences, cut sequences.
It even has tools to remove HTML tags for example, if you
click on that, nohtml.
So look at this tool.
This removes the markup language from an ASCII file.
So if you have an HTML file, feed the file to this tool and
it's able to remove all the HTML tags and gives you only
the information that's in the HTML file.
Scroll down and you can do enzyme kinetics.
There are lots of information about your sequences
that you can pull.
There are 2D structures,
composition, even gene finding.
If you have a bunch of sequence, a long stretch of
sequence, we even have tools to find genes in it.
You can do motif finding.
You can generate profiles, nucleic profiles.
You can look for repeats.
This is what I mentioned, you could even do--
there are more than one tool to perform nucleic
restriction.
So click on the remap.
You click on any of these tools and that brings you to
the specific tool's page, individual page.
And remap displays restriction enzyme binding sites in a
nucleic acid sequence.
You can paste in your own sequence here.
By default this is the enzyme list that is has got.
But you choose either one if you have a list of enzyme that
you want to cut.
You can choose that.
These are some of the parameters and once you've set
everything, if you click this button, run remap, it's that's
going to run and give you the results.
This is just an example.
This is the same way that you find information about every
single tool.
So you have it, you have an input.
So let's go down protein motif, for example, fuzzpro.
So there's a small description about that.
And if you're interested in a detailed help manual, read
this manual link here.
It gives you a detailed description about the input
format, output format, and all the different parameters.
All the stuff is up here, including an example file.
So input your sequence, and you can
input your search pattern.
So fuzzpro for example it searches for patterns in
important sequences.
So input your sequence here, the search pattern and then
choose your output format, what format you want, and then
run fuzzpro.
That should give you the output for diagram.
So like I said, there are a number of tools here.
You will always, most probably, will find a tool
that you're looking for in EMBOSS collection.
So if you have any questions, one of the first and best
places to go, to start with, is EMBOSS.
I hope you will really be able to use EMBOSS and
have fun with it.
Thank you.