CONTENTS

PAGE
S.NO EXPERIMENT
NO

1. INFORMATION SEARCH USING WWW

2. PHARMACEUTICAL RESOURCES

3. SIMILARITY SEARCHING USING BLAST

4. PAIR WISE LOCAL ALIGNMENT OF TWO SEQUENCES

USING WATER ALGORITHM OF EMBOSS

5. PAIR WISE GLOBAL ALIGNMENT OF TWO SEQUENCES

USING NEEDLE ALGORITHM OF EMBOSS

6. MULTIPLE SEQUENCE ALIGNMENT USING CLUSTAL-O

7. PHYLOGENETIC ANALYSIS USING CLUSTAL O

8. DOWNLOADING AND INSTALLING A PROGRAM

Ex.No: 1 Date:

INFORMATION SEARCH USING WORLD WIDE WEB

Aim:

Retrieve of structural and pharmacological information from PubChem database

Introduction:

pubChem, released in 2004, provides information on the biological activity of small

molecules. It is a component of NIH’s Molecular Libraries Roadmap Initiative.

PubChem is organized as three linked database within the NCBI’s Entrez information
retrieval system. These are PubChem substance, PubChem compound and PubChem
bioassay. PubChem also provides a fast chemical structural similarity search tool. More
information about using each compound database may be found using the inks in
homepage.

Links from PubChem’s chemical structure records to entrez database provide

information on biological properties. These include links to PubChem scientific
literature and NCBI’s protein 3D structure resource. Linked to PubChem’s bioassay
database present the results of biological screening. Links to depositor web sites provide
future information. A PubChem FTP site, download facility, power user gateway
(PUG), standardization service, score matrix service, structure clustering, and
deposition gateway are also available.

Pubchem provide tips and example code to allow users to add PubChem search tool
(free) in their sites. A pubchem publication site provides links to published articles.

Procedure:

1. Retrieving structure of a compound:

 Step 1: open URL: http://pubchem.ncbi.nlm.nih.gov/
Step 2: enter the name of the compound (paracetamol) in the search window.
Step 3: among the hits obtained click on the interested structure link to retrieve
the full information of the compound.
2. SMILES (Simplified Molecular Input Line Entry Specification) generation:
Step 1: open URL (http://pubchem.ncbi.nm.nih.gov/)
Step 2: go to chemical search.
Step 3: click on structure/substructure
Step 4: under draw structure, click on launch.
Step 5: draw the structure in the PubChem sketcher.
Step 6: copy the SMILES that are generated from PubChem sketcher.

RESULT:
SMILES generated: C1=C(C=CC(=C1)O[H])N(C(C)=O)[H]
Ex,No: 2 Date:

PHARMACEUTICAL RESOURCES

Aim:

Using World Wide Web to retrieve information

Introduction:

The World Wide Web, abbreviated as WWW and commonly known as the web, is a
system of interlinking hypertext documents accessed via the internet. With a web
browser, one can view web pages that may contain text, images, videos and other
multimedia and navigate between them by using hyperlinks.

A) Pharmacoinformatics:
a) Discipline where technology intersects with any aspects of drug delivery, from
the basic sciences (e.g. drug development or pharmacogenomics
/pharmacogenetics) to the clinical use of medications in individuals and
population.
b) Pharmacy informatics, a subset of pharmacoinformatics, typically refers to the
interface of technology with the practice of pharmacy.
c) Includes pharmacy technologies involve in the preparation, delivery, and
management of medication use within health care delivery system.
d) Includes all health care system related to medication, and clinical decision
support. Barcode and RF packing, smart pump delivery of medications,
pharmacy departmental applications, IV solution compounding system, robotics
used in the preparation and dispensing of medication of medication interfaces to
e-prescribing applications, automated dispensing machines.
e) Includes analysis and research related to data generated by the use of this
system.
f) Include the development of new technologies that improve the quality and safety
of therapeutic care relat5ed to medication use.
 Informatics in pharmacy

Basic research Biomedical informatics methods, techniques and

theories

Translation research Bio- pharmacoinformatics

Clinical pharmacoinformatics

Pharmacy informatics
Applied research

Molecular & Tissues & Individuals Populations Professional

Cellular process Organs (Patients) and society Practice

B) Drug database:

Drug databases provide comprehensive information for healthcare professional or

consumers on prescription and over the counter medications. The information includes
most important facts about the drug, detailed instructions for proper use, side effect,
warnings, precautions, food and drug interactions, dosage, over-dosage etc. The
information could be obtained by search of product name or browsing the starting letter
of the medication at the alphabetic index.

RxList

RxList is one of the best web medications index. Search for drug monographs in the
RxList drug database is possible by using generic or brand name. The search could be
also done by browsing the alphabetical listing of the medications using brand or generic
name.

Access: free

Medscape:

Medscape database contains medications and disease information. The drug search
database combines content from FDA, First DataBank and the American Society of
Health-System Pharmacists (ASHP) Pharmacopeia. Search could be done by entering
the drug or disease name.
Electronic medicines compendium (eMC)

The eMC is a comprehensive source of information about prescription and over- the –
counter medications licensed in the UK. This site provides electronic summaries of
product characteristics (SPCs) and patients information leaflets (PILs). The database
covers more than 2,500 medicines. The drug information could be found by quick
search, text search, or search by section. Quick search is the easiest and quickest way to
find information. The search could be done by using brand name, generic name or
company name.

Access: free

Druginfonet

Druginfonet provide information for health care professionals and consumers. Official
package inserts for healthcare professionals and patients are available by trade name,
generic name , manufacturers and therapeutic class. The information is applicable to the
US and has been approved by the U.S. Food and drug administration.

Access: Free

RxMed:

RxMed is a comprehensive, peer-reviewed web resource offering drug and disease

information for physicians and patients, as well as access to various medical products
and services. Detailed monographs are available for over 3,000 prescription drugs. The
listings cover general pharmacology, indications, warnings, dosage and adverse effects
information for each monograph.

Access: Free

Drugs.com:

Drugs.com is a comprehensive and up to date information resource for medical

professionals and consumers providing convenient and reliable information on over
24,000 approved prescription drugs, over-the-counter medications, and natural products.

Access: free registration for access to the professional’s information.

CONSUMER-ORIENTED DRUG DATABASE:

MedlinePlus:
MedlinePlus drug information database provides consumer-oriented information on
thousands of prescription and over the counter medications using medmaster, a product
of American society of health system pharmacists (ASHP). The information could be
found by browsing the starting letter of a generic or brand name drug.

Additional drug information could be found at drug therapy page.

Access: Free

MedicineNet:

The drug database of medicinenet offers patient-oriented and reliable medical

information on over 2500 common medications, which include pharmaceutical class
and mechanism of action, indication, dosing, drug interactions side effect, etc. The
information could be obtained by search or browsing the starting letter of the
medication.

Access: Free

Health square:

Healthsquare drug database offers comprehensive information on prescription

medications. The information is supplied by the PDR family guide to prescription
drugs, and includes most important fact about this medication, detailed instructions for
proper use, side effects, warning, interactions, dosage, over dosage. The information
could be obtained by search of product name or browsing the starting letter of the
medication at the alphabetic index. Other possibility is to brows the conditions index
where the products are listed by their commonly prescribed indications.

Access: Free

SafeMedication:

Safemedications.com provides consumer-oriented searchable database (MedMaster

TM). The information in this database is based on ASHP’s medication teaching manual:
the guide to patient drug information, used in patient-education programs conducted by
health-care professionals. The database, which includes more than 900 brand name and
generic medications, enrich the information provided by the physicians and the
pharmacists. The consumer information includes indications, instructions for use,
precautions, and side effects. The information could be found by search using generic or
brand name.

Access: Free

WebMD

The WebMD directory provides comprehensive patient-oriented information on

prescription and over-the-counter medications. The information includes drug class,
indications, dosing, overdose, interactions, warnings, precautions, side effects. The
leaflets could be found by search by brand or generic name, or by condition, or
browsing the medications by name. WebMD provides also quality health information.

Access: Free

Mayoclinic.com

Provides comprehensive information on prescription medications and over-the-counter

pharmaceuticals from micromedex, as well as information on herbs, vitamins and other
supplements from natural standard. The information could be obtained by search or
browsing the starting letter of the medication.

Access: Free
Ex no: 3 Date:

SIMILARITY SEARCHING USING BLAST

AIM:
To find a similar to the sequence from PDB database

INTRODUCTION:
BLAST is a heuristic approach developed at the NCBI for local alignment that
can effect relationships among the sequence which share only isolated regions of
similarity

PRINCIPLE:
BLAST is a process involving three steps process
1. Find the list of high scoring words (w). BLAST takes each word from the query
sequence (typically w is 3 for amino acid and 11 for nucleotide), and locates
similar words in the current test sequence
2. Compare the word list to the database and identify the exact matches. If similar
words are found are found, BLAST tries to expand the alignment to the adjacent
words, without allowing for gaps.
3. After all the words are tested; a set of maximal segment pairs (MSP) is chosen that
database sequence. Several short, non-overlapping MSPs may be combined in a
statistical test to create a larger, more significant match

PROCEDURE:
Running the NCBI blastp
1. Point your browser to the NCBI BLAST server at
http://blast.ncbi.nlm.nih.gov/blast.cgi
2. Under the protein BLAST heading click the standard protein-protein BLAST
(BLAST P) .link
3. Paste your sequence in the search window
4. Choose PDB from the choose database pull down menu
5. Click the blast button
AN OVER VIEW OF THE BLAST OUTPUT
The section which appeal in the BLAST out put
A graphic display:
1. Each represents the portion of sequence. Similar to the query sequence and the
region of the sequence where the similarity occurs
2. Red bars indicate most similarity sequence
3. Pink bars indicate the matches which are less good
4. Green bars indicate the matches that are not impressive at all
5. Blue and black bars indicate the matches that have the worst score
6. Red, green and pink once are usually good ones
The hit list:-
It tells us weather our sequence looks like something already in the database are not we
can trust it is a good hint
Each line contain 4 important features
1. The sequence accession number and the name :-
The hyper link takes us to the database entry that contain this sequence
In this entry we may find very important annotated information describing the
sequence
2. Description:
A description that comes from the annotation lets us know at a glance whether
this binding could be interesting for us.
3. The bit score:
A measure of the statistical significance of the alignment
The high the bit score the most similar the two sequences
Matches below 50 bits are very unreliable
4. The E- value (the expectation value):
This is a statistical value denoted by the letter E used to report matches are
expected. If the statistical value for the match is greater than the E-value, it will
not show any match. The smallest the E-value the closer the match and more
confidence we can have that this hit is really homologous to our query.
The alignments:
BLAST displays the alignment for a BLAST search below hit list. In every
alignment we can find the following features,
1. The % identity: this is a concrete substitute for the E-value. More than 25%
identity denotes homology.
2. Length: this is the length of alignment which indicates how long two segments
of the sequences that BLAST has aligned are.
3. The top sequence in the alignment is query. The bottom sequence is the hit (or
subject).In the line in between the two sequences,
+---------------similarity
A letter-------identity
Space---------mismatch
xxxxx---------masked region (region of low complexity)
4. The numbers: numbers to the side of the sequences indicate the co-ordinates of
the match on the query sequence and on the hit list.
5. The parameters: it keeps track of the changes made to default parameters.
RESULT:
Input:
>gi|695898490|cytochrome b (mitochondrion) [Homo sapiens neanderthalensis]
MTPMRKINPLMKLINHSFIDLPTPSNISAWWNFGSLLGACLILQITTGLFLAMHYSPDASTAFSSIAHIT
RDVNYGWIIRYLHANGASMFFICLFLHIGRGLYYGSFLYSKTWNIGIILLLATMATAFMGYVLPWGQMSF
WGATVITNLLSAIPYIGTDLVQWIWGGYSVDSPTLTRFFTFHFILPFIIAALAALHLLFLHETGSNNPLG
ITSHSDKITFHPYYTIKDALGLFLFLLSLMTLTLLSPDLLGDPDNYTLANPLNTPPHIKPEWYFLFAYTI
LRSVPNKLGGVLALLLSILILAMIPILHVSKQQSMMFRPLSQSLYWLLAADLLILTWIGGQPVSYPFIII
GQVASVLYFTTILILMPTISLIENKMLKWA
Ex. No: 4 Date:

PAIR WISE LOCAL ALIGNMENT OF TWO SEQUENCES USING WATER

ALGORITHM OF EMBOSS

AIM

Comparison of given two protein sequences by using EMBOSS local alignment search
tool with smith-waterman algorithm.

Introduction:

EMBOSS is used to compare two sequences. When whole length comparison of the
sequences is required Needleman algorithm can be used. For local alignment, smith-
waterman algorithm can be used.

Principle:

Local alignment:

Water uses the smith-waterman algorithm (modified for speed enhancement) to

calculate the local alignment of a sequence to one or more other sequences. The gap
inserted penalty, gap extension penalty and substitution matrix used to calculate the
alignment are specified. The output is a standard EMBOSS alignment file.

Input:

>sequence 1

MKPGTRGTFVPVNHVRTAAKPSASTLLARVCGSAVLFAGAASAQPAMAQQRSFPPRPTGTERQIDVRATAALEYNDNVV
LNDPRIAQGAPRDDVSAAPSLDLNILLPRPTGSVYVSGNIGYRFYRRYSYLNREMISLSGGIDQRLASCVVHGDLGYQRRLS
DLSNLSLQDSPESFKNTEEVRRYATDIGCGGQYGLRPAVAFSRTEVRNSRSERSYADSNTNMVTAQLGLLVPAIGTVSVFG
RYADSSYPRRPVPAGSERDGLKSYAAGLQLERSVGQRLDFRGSANYTKADPKLRGTRGFSGFGFDLSAAYKGDPFTVLLS
GSRSAEPSQLFFISYEVVTTLTGSVTRQLGDRTSLSLRASKTWRDLSASELFPNAPRVGNNDIGSILASAVYRPSRRLRFSLE
GGYERRTSNVQLYQY RAKRINLTTSLSL

>sequence 2

MKQFSVMSAAATAALMIPQAALSQTEVEVPPDGLRVRPTVRLLYDSNILRQNDDLVTAEQDDLRITPSVDVTYRRQFGLH
RLTVIGSAGYDFHQRFEFLDRERVSLQADADLSVSGYCHVQPRARLNFAQSNLSDQGVVVGNTQRTQDYRVAVDCEKPY
GFFPVAAMGYLNTSNSASSRRIFDIDTSTAMAGIGYSKASLGEIRATFQYERFRRPNADEAIAGLRDGAENYRAGILFRRAV
APRLSWQLGANYFKTKPRAPGIADFSGLGVEAQAVYTPSNRLSILLDVDRSSRNQSNTGATYIVQTDFSLRGNLKLGARSG
LSIGGSYSRRSFKGELQLDTPLLRRSDRTRAVFAGYRYQLRSRLNAGAEIRHEWRTTAVDQFRYKSTSGLLFVGLDL

Procedure:
Parameter used:

1. Method: EMBOSS water(local)

2. Gap open: 10.0
3. Gap extend: 0.5
4. Molecule: protein
5. Matrix : blosum62
 Above parameters were set.
 Two sequences, which have to be aligned, are given in the “sequence 1 and
sequence 2” window.
 Click run button.

RESULT:
Ex.No: 5 Date:

PAIWISE GLOBAL ALIGNMENT OF TWO SEQUENCES USING NEEDLE

ALGORITHM OF EMBOSS

AIM: Comparison of two sequences by using Needle global alignment algorithm

INTRODUCTION

EMBOSS is used to compare two sequences. Needleman- Wunsch algorithm can be

used when comparison of whole length of two sequences in required. For local
alignment, smith waterman algorithm can be used

PRINCIPLE

GLOBAL ALIIGNMENT

Needle reads two input sequences and writes their optimal global sequence alignment to
file .it uses the Needleman- Wunsch alignment algorithm to find the optimum alignment
(including gaps) of two sequences along their entire length .The algorithm uses a
dynamic programming method to ensure the alignment is optimum, by exploring all
possible alignments and choosing the best. A scoring matrix read that contains values
for every possible residue or nucleotide match. Needle finds the alignment with the
maximum possible score where the score of an alignment is equal to the sum of the
matches taken from the scoring matrix, minus a penalties arising from opening and
extending gaps in the aligned sequences. These substitution matrix and gap opening and
extension penalties are user specified.

INPUT

>seq1

MKPGTRGTFVPVNHVRTAAKPSASTLLARVCGSAVLFAGAASAQPAMAQQRSFPPRPTGTERQIDVRATAALEYNDNVV
LNDPRIAQGAPRDDVSAAPSLDLNILLPRPTGSVYVSGNIGYRFYRRYSYLNREMISLSGGIDQRLASCVVHGDLGYQRRLS
DLSNLSLQDSPESFKNTEEVRRYATDIGCGGQYGLRPAVAFSRTEVRNSRSERSYADSNTNMVTAQLGLLVPAIGTVSVFG
RYADSSYPRRPVPAGSERDGLKSYAAGLQLERSVGQRLDFRGSANYTKADPKLRGTRGFSGFGFDLSAAYKGDPFTVLLS
GSRSAEPSQLFFISYEVVTTLTGSVTRQLGDRTSLSLRASKTWRDLSASELFPNAPRVGNNDIGSILASAVYRPSRRLRFSLE
GGYERRTSNVQLYQY RAKRINLTTSLSL

>seq2

MKQFSVMSAAATAALMIPQAALSQTEVEVPPDGLRVRPTVRLLYDSNILRQNDDLVTAEQDDLRITPSVDVTYRRQFGLH
RLTVIGSAGYDFHQRFEFLDRERVSLQADADLSVSGYCHVQPRARLNFAQSNLSDQGVVVGNTQRTQDYRVAVDCEKPY
GFFPVAAMGYLNTSNSASSRRIFDIDTSTAMAGIGYSKASLGEIRATFQYERFRRPNADEAIAGLRDGAENYRAGILFRRAV
APRLSWQLGANYFKTKPRAPGIADFSGLGVEAQAVYTPSNRLSILLDVDRSSRNQSNTGATYIVQTDFSLRGNLKLGARSG
LSIGGSYSRRSFKGELQLDTPLLRRSDRTRAVFAGYRYQLRSRLNAGAEIRHEWRTTAVDQFRYKSTSGLLFVGLDL

PROCEDURE:

Parameters used
1. METHOD: EMBOSS::Needle (global)
2. GAP OPEN :10.0
3. GAP EXTEND:0.5
4. MOLECULE: Protein
5. MATRIX:Blosum62

PROCEDURE: Above parameters were set. Two sequences, which have to be

aligned, are given in the “sequence”&”sequence2” windows.

RESULT
Ex.No; 6 Date:

MULTIPLE SEQUENCE ALIGNMENT USING CLUSTAL-O

AIM: To produce multiple sequence alignment of different protein sequence

INTRODUCTION

Clustal-Omega is a general purpose multiple sequence alignment (MSA) program for

proteins. It produces high quality MSAs and is capable of handling data-sets of
hundreds of thousands of sequences in reasonable time.
In default mode, users give a file of sequences to be aligned and these are clustered to
produce a guide tree and this is used to guide a "progressive alignment" of the
sequences. There are also facilities for aligning existing alignments to each other,
aligning a sequence to an alignment and for using a hidden Markov model (HMM) to
help guide an alignment of new sequences that are homologous to the sequences used to
make the HMM. This latter procedure is referred to as "external profile alignment" or
EPA.
Clustal-Omega uses HMMs for the alignment engine, based on the HHalign package
from Johannes Soeding [1]. Guide trees are made using an enhanced version of mBed
[2] which can cluster very large numbers of sequences in O(N*log(N)) time. Multiple
alignment then proceeds by aligning larger and larger alignments using HHalign,
following the clustering given by the guide tree.
In its current form Clustal-Omega can only align protein sequences but not DNA/RNA
sequences. It is envisioned that DNA/RNA will become available in a future version.
PRINCIPLE:

Clustal-O fallows three steps.

1. Perform pair –wise alignment for all sequences.

2. Use the alignment scores that gives a Phylogenetic tree using the neighbor-
joining (NJ- METHODS)
3. The sequences are aligned using the phylogenetic relationships indicated by the
tree.

INPUT: MYOSIN heavy chain protein sequences from different organisms.

Multiple sequences were uploaded in FASTA format, which consists of a one line
header starting with a “>”symbol, followed by the sequence name /description. The
sequences then enter the on new file

PROCEDURE:

1. Upload Myosin heavy chain sequences in FASTA format

2. Set all the parameters used
EMAIL ID: Enter your email for email results option

ALIGNMENT TITTLE: MHC sequences

RESULTS: Interactive

ALIGNMENT: full

FAST ALIGNMENT SEARCH OPTIONS: KTUP, WIDOW, SCORE, TOPDLAG,

PAIRGAP

MULTIPLE SEQUENCE ALIGNMENT OPTIONS:

1. MATRIX: Default (Gonnet250)

2. GAPOPEN: Default(10.0)
3. NO END GAPS: Default (Yes)
4. GAP EXTENSION: Default (0.2)
5. GAP DISTANCES: Default (4)
6. ITERATION: Default (None)
7. NUMITER: Default (1)

RESUL:

Fig: Part of the alignment of Myosin heavy chain sequence

Ex.No; 7 Date:

PHYLOGENETIC ANALYSIS USING CLUSTAL O

AIM: To construct the phylogenetic tree of different protein sequence by using Clustal-
O online tool.

INTRODUCTION

Phylogenetic tree analysis of protein sequence is important tools in studying sequence..

This is very use full in designing experiment to test and modify the function of specific
protein, in predicting the function and structure of protein .and identifying new member
of protein families. Cluster is fully automatic programmed for global multiple alignment
of DNA and protein sequence. The alignment is progressive evolutionary relationship
can be seen via viewing cladogarms and phylograms. The program has some adjustable
parameters with reasonably default.

PRINCIPLE:

Clustal-O fallows three steps.

1. Perform pair –wise alignment for all sequences.

2. Use the alignment scores that gives a Phylogenetic tree using the neighbor-
joining (NJ- METHODS)
3. The sequences are aligned using the phylogenetic relationships indicated by the
tree.

INPUT: MYOSIN heavy chain protein sequences from different organisms.

Multiple sequences were uploaded in FASTA format, which consists of a one line
header starting with a “>”symbol, followed by the sequence name /description. The
sequences then enter the on new file

PROCEDURE:

1. Upload Myosin heavy chain sequences in FASTA format

2. Set all the parameters used

EMAIL ID: Enter your email for email results option

ALIGNMENT TITTLE: MHC sequences

RESULTS: Interactive

ALIGNMENT: full

FAST ALIGNMENT SEARCH OPTIONS: KTUP, WIDOW, SCORE, TOPDLAG,

PAIRGAP

MULTIPLE SEQUENCE ALIGNMENT OPTIONS:

3. MATRIX: Default (Gonnet250)

4. GAPOPEN: Default(10.0)
5. NO END GAPS: Default (Yes)
6. GAP EXTENSION: Default (0.2)
7. GAP DISTANCES: Default (4)
8. ITERATION: Default (None)
9. NUMITER: Default (1)

RESULT:

Fig: Phylogenetic analysis using CLUSTAL O

Ex. No: 8 Date:

DOWNLOADING AND INSTALLING A PROGRAM

Aim:

To download and installing the Swiss-PDB Viewer tool

Procedure:

1. Go to SPDBV home page. http://spdbv.vital-it.ch/

2. Click on download option in the left side of the page.

3. Click on the disclaimer agreement.
4. Select the operating system you are using.
 5. Go to save option.
6. Save in a specific directory.
7. Double click spdbv application icon to open installed programme.

RESULT:

The SPDBV program was downloaded and installed into the system.