Molecular Biology

1. Nucleotide Sequence Analysis
Mohamed E. Hasan
Ph.D. Bioinformatician
Department of Bioinformatics, GEBRI

2. COURSE
CONTEN
T
(LECTUR
E):
Review of DNA
replication,
transcription, and
translation, Genome
organization
Week 2 Review of
Sequencing methods
)Sanger sequencing)
Week 3 NGS Data
Analysis
Week 4 Introduction to
DNA and protein
databases, data storage,
file formats, information

3. Week 5 Consensus sequences, Finding
genes and open reading frames in DNA
sequences
Week 6 Introduction to Proteomics
Week 7 Prediction of protein structure
and function
Week 8 Prediction of protein structure
and function continued, Comparative
genomics

4. 4

5. BIOINFORMATICIAN VS BIOLOGIST
Bioinformatician Biologist

6. BIOINFORMATICIAN CATEGORIES

7. 7
Central Paradigm in Molecular Biology

8. 8

9. IMPORTANCE
 DISCOVERY, DEVELOPMENT AND IMPLEMENTATION OF
COMPUTATIONAL ALGORITHMS AND SOFTWARE TOOLS
AGRICULTURE AND HEALTHCARE SECTORS WITH
SEVERAL SPINOFFS.
IN A DEVELOPING COUNTRY LIKE INDIA,
BIOINFORMATICS HAS A KEY ROLE TO PLAY IN AREAS
LIKE AGRICULTURE.
IN THE PHARMACEUTICAL SECTOR, IT CAN BE USED TO
REDUCE THE TIME AND COST INVOLVED IN DRUG
DISCOVERY PROCESS.
IN MEDICINE SECTOR, BIOMARKER DISCOVERY OF
COMPLEX DISEASE

10. Molecular
biology: definition
• Molecular biology is the
study of molecular
underpinnings of the
process of replication,
transcription and
translation of the genetic
material.

11. Components involve in molecular biology
DNA RNA
Protein

13. Deoxyribonucleic
acid (DNA)
• DNA is a nucleic acid that
contains the genetic
instructions used in the
development and
functioning of all known
living organisms and
some viruses.
• DNA is a set of blueprints
needed to construct other
components of cells, such
as proteins and RNA
molecules.

14. • Two long strands makes
the shape of a double helix.
• two strands run in opposite
directions to each other and
are therefore anti-parallel.
• Chemically, DNA consists
of two long polymers of
simple units called
nucleotides, with
backbones made of base,
sugars and phosphate
groups.
Fig : DNA double helix

18. • The DNA double helix is stabilized by hydrogen bonds between the
bases attached to the two strands.
• One major difference between DNA and RNA is the sugar, with the
2-deoxyribose in DNA being replaced by the alternative pentose
sugar ribose in RNA.
Ribose

19. Ribonucleic acid (RNA)
• RNA is a biologically important type of molecule that consists of a
long chain of nucleotide units.
• Each nucleotide consists of a nitrogenous base, a ribose sugar, and
a phosphate.

23. Gene : Unit of heredity
• The DNA segments that
carries genetic information are
called genes.
• It is normally a stretch of DNA
that codes for a type of protein
or for an RNA chain that has a
function in the organism.
• Genes hold the information to
build and maintain an
organism's cells and pass
genetic traits to offspring.

35. What’s the Next Step?
• After sequence is determined, then what?
• Make sense of it by comparing with other related
(homologous) sequences
– Multiple Sequence Alignment

36. The design, construction and use of software tools to
generate, store, annotate, access and analyse data and
information relating to Molecular Biology
Bioinformatics
OR
Biologists doing “stuff” with computers?

37. Sequence submission
• Data mainly direct submissions from the
authors.
• Submissions through the Internet:
– Web forms.
– Email.
• Sequences shared/exchanged between the 3
centers on a daily basis:
– The sequence content of the banks is identical.

38. Nucleotide Sequence Databases
 NCBI (National Center for Biotechnology
Information)
 EMBL (European Molecular Biology Laboratory)
 DDBJ (DNA DataBank of Japan)

39. Protein Sequence Database
 SWISS-PROT
 TrEMBL

40. 40
GenBank Flat File
Features (AA seq)
DNA Sequence
Heade
r
•Title
•Taxonomy
•Citation
LOCUS AF115338 591 bp DNA linear BCT 19-AUG-1999
DEFINITION Pseudomonas fluorescens ECF sigma factor SigX (sigX) gene, complete
cds.
ACCESSION AF115338
VERSION AF115338.1 GI:4959391
KEYWORDS .
SOURCE Pseudomonas fluorescens.
ORGANISM Pseudomonas fluorescens
Bacteria; Proteobacteria; gamma subdivision; Pseudomonadaceae;
Pseudomonas.
REFERENCE 1 (bases 1 to 591)
AUTHORS Brinkman,F.S., Schoofs,G., Hancock,R.E. and De Mot,R.
TITLE Influence of a putative ECF sigma factor on expression of the major
outer membrane protein, OprF, in Pseudomonas aeruginosa and
Pseudomonas fluorescens
JOURNAL J. Bacteriol. 181 (16), 4746-4754 (1999)
MEDLINE 99369842
PUBMED 10438740
REFERENCE 2 (bases 1 to 591)
AUTHORS De Mot,R.
TITLE Direct Submission
JOURNAL Submitted (04-DEC-1998) F.A. Janssens Laboratory of Genetics,
Applied Plant Sciences, K. Mercierlaan 92, Heverlee B-3001, Belgium
FEATURES Location/Qualifiers
source 1..591
/organism="Pseudomonas fluorescens"
/strain="M114"
/db_xref="taxon:294"
gene 1..591
/gene="sigX"
CDS 1..591
/gene="sigX"
/codon_start=1
/transl_table=11
/product="ECF sigma factor SigX"
/protein_id="AAD34329.1"
/db_xref="GI:4959392"
/translation="MNKAQTLSTRYDPRELSDEELVARSHTELFHVTRAYEELMRRYQ
RTLFNVCARYLGNDRDADDVCQEVMLKVLYGLKNLEGKSKFKTWLYSITYNECITQYR
KERRKRRLMDALSLDPLEEASEEKALQPEEKGGLDRWLVYVNPIDRGILVLRFVAELE
FQEIADIMHMGLSATKMRYKRALDKLREKFAGETET"
BASE COUNT 157 a 133 c 170 g 131 t
ORIGIN
1 atgaataaag cccaaacgct atccacgcgc tacgaccccc gcgagctctc tgatgaggag
61 ttggtcgcgc gctcgcatac cgagcttttt cacgtaacgc gcgcctatga agaactgatg
121 cggcgttacc agcgaacatt atttaacgtt tgtgcgagat atcttgggaa cgatcgcgac
181 gcagacgatg tctgtcagga agtcatgttg aaggtgctgt atggcctgaa gaacctcgag
241 gggaaatcga agttcaaaac gtggctctac agcatcacgt acaacgaatg tattacgcag
301 tatcggaagg aacggcgaaa gcgtcgcttg atggacgcat tgagtcttga ccccctcgag
361 gaagcgtccg aagaaaaggc gcttcaaccc gaggagaagg gcgggcttga tcgctggctg

41. •
Major research areas
• 1- Sequence analysis
• 2- Computational evolutionary biology
• 3- Gene prediction
• 4- Epitope prediction
• 5- Prediction of protein structure