Muliple Sequence Alignment

go to this page to align your sequences using ClustalW paste all of your sequences or upload your text file to get your alignment result
http://www.ebi.ac.uk/Tools/es/cgi-bin/clustalw2/result.cgi?tool=clustalw2&jobid=clustalw2-20101030-1758594671&poll=yes

This is the multiple sequence alignment of the selected sequences

Read more »

Muliple Sequence Alignment

For Multiple sequence Alignment you need Fasta sequence for this go to ncbi for nucleotide or at expasy server for protein sequence but now I am going to work with proteins so go to www.expasy.org
enter your query for which you want to retrieve the sequences
or you can also go to uniprot which in my opinion is easy to use and get fasta sequence so go to uniprot and enter protein hemoglobin and get different entries of this protein click them and get fasta sequence like this

and select many proteins and get their fasta formats like this
 click on fasta and http://www.uniprot.org/uniprot/P68871.fasta
copy and paste these fasta sequences of many proteins in a text file and collect all these sequences in a text document.
In this format I pasted my all sequences in my notepad

Read more »

ClustalW:

ClustalW is a general purpose multiple sequence alignment program for DNA and proteins it produces biologically meaning full multiple sequence alignments of divergent sequences it calculates the best match for selected sequences that lines up so that the identities and similarities and differences and evolutionary relationships can be seen via viewing cladograms or phylograms.

Read more »

PDB structures part 3

The previous page contains the PDB ID of the particular protein
http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?uid=34605
get this PDB ID and entered into PDB and get the same 3D structure of the protein

http://www.rcsb.org/pdb/explore/explore.do?structureId=1WYM

Read more »

PDB structures part 2

As we entered the gene name to ncbi and get complete information about the gene and also get the protein which is encoded by the gene. Get this name and entered into the structure database in ncbi. http://www.ncbi.nlm.nih.gov/sites/structure/?term=Transgelin-2

 the protein entered is Transgelin-2
http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?uid=34605
view 3D structure using cn3d which is a structure viewer I mentioned in my very previous tutorial how to use and download cn3d 4.0 to your systems

Read more »

PDB Structures

As you know PDB is used for finding the structure of different proteins for this I have selected different genes and get their proteins  you can see.
I select three Tumor Supressor Genes

1.

p16^INK4a

^2.

p53

3.

RB - the retinoblastoma gene

entered these genes in ncbi http://www.ncbi.nlm.nih.gov/

select nucleotide in search and enter  the gene name

p16^INK4a get this page http://www.ncbi.nlm.nih.gov/nuccore/NM_001001522.1

 

Read more »

3.PDB:

PDB is a protein data bank it contains information about the structure and function of the reported proteins. Not only the information about the protein is present but also of many macromolecules like nucleic acids and carbohydrates.
How to Search PDB:
go to http://www.rcsb.org/pdb/explore/motm.do
enter PDB ID if you don't know the ID then enter the text methylenetetrahydrofolate reductase to get the structural information of that protein
I entered this text then get this result go to this page http://www.rcsb.org/pdb/results/results.do?outformat=&qrid=FA02BFE5&tabtoshow=Current

Read more »

2. PUBCHEM:

http://pubchem.ncbi.nlm.nih.gov/
if you enter chlorpropamide which is the molecule use for the treatment of Type II diebetes it will give complete information about the structure and function of the molecule.

 PubChem provides information on the biological activities of small molecules. It is a component of NIH's Molecular Libraries Roadmap Initiative.
visit this page I have entered the molecule name
http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=2727&loc=ec_rcs

Read more »

Out put:

I entered the disorder diabetes melitis
and it gives the results that you  get by accessing this page
http://www.drugbank.ca/drugs/DB00672

Read more »

1. LIGAND PREPARATION:

Ligand preparation further divided into different heading namely, ligand retrieval or collection, liand conversion and ligand analysis

a. Ligands Collection:
1. DRUGBANK :http://www.drugbank.ca/
first go to this link enter your protein or condition like any disease and disorder it will give you complete information about the drug which is designed for the particular purpose eg enter anxiety disorder in drugbank it will give you different ligands of that particular disorder and protein and also gives complete information about the target protein.
The DrugBank database is a unique bioinformatics and cheminformatics resource that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information. The database contains nearly 4800 drug entries including >1,480 FDA-approved small molecule drugs, 128 FDA-approved biotech (protein/peptide) drugs, 71 nutraceuticals and >3,200 experimental drugs. Additionally, more than 2,500 non-redundant protein (i.e. drug target) sequences are linked to these FDA approved drug entries. Each DrugCard entry contains more than 100 data fields with half of the information being devoted to drug/chemical data and the other half devoted to drug target or protein data.

Read more »

Steps Involved in Drug Designing

Drug designing steps were usually divided into steps as follows:

I. LIGAND PREPARATION

II. RECEPTOR PREPARATION

III. DOCKING

IV. BINDING AFFINITY STUDIES

Read more »

DRUG DESIGNING

Drug designing basically of two types namely ligand based approach or receptor based approach. In both the case the point of centre only differ but requirement of receptor and ligand essential in both the case.  

 

he shortcoming of traditional drug discovery; as well as the allure of a more deterministic approach to combating disease has led to the concept of "Rational drug design" (Kuntz 1992). Nobody could design a drug before knowing more about the disease or infectious process than past. For "rational" design, the first necessary step is the identification of a molecular target critical to a disease process or an infectious pathogen. Then the important prerequisite of "drug design" is the determination of the molecular structure of target, which makes sense of the word "rational".

In fact, the validity of "rational" or "structure-based"drug discovery rests largely on a high-resolution target structure of sufficient molecule detail to allow selectivity in the screening of compounds. Simple flowchart for drug designing shown in the figure:

Read more »

HTML Frames:

I told you people about the html frames there is the same thing but with the slight variation
<html>
<frameset rows="20%,80%">
<frame src="file:///E:/anny.html" name="frame1" noresize="noresize">
<frame src="http://www.islamickorner.com">
</frameset>
</html>
one new thing is noresize attribute which means you can not resize your page as previously by dragging its size is fixed you can check it by dragging your page it can't be happened.
the out put is as:

Read more »

HTML Images2:

I told you how to link your page to other sites by using the <a href> tag so I have an assignment for you design a page in which you click on image to access the new page instead of a text eg you click Islamickorner to access this site but now click an image to access this site so try it
out put is as:

 click the second image to get the next page
this is the next page or site which is accessed by the link behind that image its code is as:

<a href="http://www.bermuda-online.org/roses2.gif"><img src="file:///C:/Documents%20and%20Settings/Administrator/My%20Documents/My%20Pictures/roses2.gif" height="200" width="200" border="10"></img></a>

Read more »

HTML Images:

When you want to insert images to your web page:
<img src="enter your source or link of your image.jpg" alt="if your source is not available so enter any other link or display the message for the user image is not available.jpg" width="200" height="200" border="2"></img>
height of the pic width of the pic and border is for bordering the pic
the code is as
<center>
<img src="file:///C:/Documents%20and%20Settings/Administrator/My%20Documents/My%20Pictures/roses2.gif" alt="image not available" height="200" width="200" border="2"></img></center>

Read more »

HTML Comment:

comments are actually for users they are not interpreted by your browser they are only for the convience of the developer for future use to remember for which purpose he/she used the tags.
<!--comment like this is the tag for comments not displayed on your web page-->
<hr>a horizontal line will be displayed on your page to divide it</hr>

<!--comment-->
<hr></hr>

Read more »

HTML Lists:2:

Previously I told you about the ordered and ordered lists now there are some other examples the code is as:

<ol>
<li type="a">lowercase letter</li>
<li type="A">uppercase letter</li>
<li type="i">lowercase roman</li>
<li type="I">upppercase roman</li>
<li type="1">numeric</li>
</ol>
<ul>
<li type="square">square</li>
<li type="disc">disc</li>
<li type="circle">circle</li>
</ul>

Read more »

HTML Lists:

Now the next is HTML Lists when you want to generate the lists of your items these lists can be ordered in the form of numbers or letters and in an unordered form also so the ordered list is
<ol>ordered list</ol>
<li>milk</li>
li means list items

<ul></ul>unordered list
<li>milk</li>
code is as:
<ul>
<li>coffee</li>
<li>milk</li>
</ul>
<ol>
<li>coffee</li>
<li>milk</li>
</ol>

the out put is as:

Read more »

HTML Tables:

Now we are going to generate tables in HTML
First use the table tag <table border=1>
border=1 means the border of the table and its size
<tr> table row <td>table data</td> </tr>
now the code is as
</table>
<html>
<body>
<table border="1">
<tr>
<td><h1>Roll#</h1></td><td><h1>Name</h1></td><td><h1>E-mail</h1></td>
</tr>
<tr>
<td>1323</td><td>Quratt ul ain </td><td>Quratt786@live.com</td>
</tr>
<tr>
<td>1171</td><td>Ubaid ur rehman</td><td>obaid1986@live.com</td>
</tr>
</table>
</body>
</html>

out put is

Read more »

HTML Tutorial part 4.1

you can also do this by splitting your page in columns like this

<frameset cols="50%,50%">
<frame src="a.html">
<frame src="b.html">
</frameset>
now I have a small assignment for you to check what you have learned generate a code for the following output:

for your convinience the source code of this page is
 as :
<html>
<frameset rows="25%,75%">

<frame src="b.html">

<frameset cols="25%,75%">
<frame src="b1.html">
<frame src="http://www.ncbi.com">
</frameset>
</html>
Hope you will like it so please leave your comments and give your feedbacks regards Quratt ul ain Siddique

Read more »

HTML Tutorial part 4

HTML Frames: some times you want to display your web pages at a time on the same window so use
Frames like this:
select or use a new note pad and write the code like this
<html>
<frameset rows="25%,75%">
<frame src="http://www.islamickorner.com">
<frame src="a.html">
</frameset>
</html>
The output will be:

Read more »

HTML Tutorial part 3

If you want to link your page to other web pages so use link tag which is

<a href="http://www.islamickorner.com>Islamic Korner</a>

Read more »

HTML Tutorial part 2

<body style="background-color:yellow">
means your background color will be yellow
<p style="font-family:times new roman;font-size:20px">paragraph style will be times new roman and size will be 20 pixels font-family : this is the equal sign seperated by ; then other element </p>

Read more »

Output of the previous tutorial

Read more »

HTML Tutorial part 1

first write on page
<html>
the every thing which is done on  your web page will be inside these tags you are actually defining the body of html </html>
this will be the <> starting tag and </> this will be the ending tag to complete your task. Each starting tag must have an ending tag don't forget it. so <title>My web page</title> this title MyWeb Page will not appear on your page it will appear on your task bar and in your title bar. Now <body>this is the body of your page in which you perform your all functions.
<h1>Heading 1</h1> this is the heading of your page
<p>paragraph</p>
</body>
eg the body of  your source code will be like this
<html>
<title>My web page</title>
<body>
<h1>Bioinformatics Department</h1>
<p>description about department of Bioinformatics</p>
</body>
</html>

lets try it and wait for next parts of this tutorial.

Read more »

Learn HTML: HTML Tutorial

Aslam u Alaikum
now I am going to tell you about the HTML. It is actually a Hypertext Markup Language. It is not a programming language it is a mark up language which is represented by tags and easily understand by your web browser.

Now lets start with your first HTML page which will be the first initial step in designing your own web page
you can use different text editors for this language like notepad which is easily available on your PCs ,microsoft frontpage and dreamweaver but we for your convinience will use notepad
ok lets start first select a page of notepad and save it with extension .html eg "anny.html"

Read more »