1. Computer Applications and Bioinformatics

2. Generalised Picture of a Computer Motherboard
CPU Socket
DIMM (Dual In-line Memory Module)
IDE (Integrated Drive Electronics) Connector
Power Supply Connector 1
SATA Connectors
Front Panel Connectors
South Bridge
USB connectors
PCI Express
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North Bridge
Fire wire (IEEE1394) / USB (Universal Serial Bus)
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Power Supply Connector 2 15 1 14 2 13 12 3 11 4 10 5 9 8 7 6

3. What is bioinformatics?
Marriage between Computer Technology and
Biological Data

4. Definition of bioinformatics
Bioinformatics is an interdisciplinary field of science that develops methods and software tools for understanding biological data.
As an interdisciplinary field of science, bioinformatics combines computer science, statistics, mathematics, and engineering to analyze and interpret biological data.

5. Broad Applications of Bioinformatics
Sequence retrieval
Sequence alignment
Structure determination
PCR Primer Design
Construction of Phylogenetic Trees

6. Today's topic of discussion
Sequence retrieval
Sequence alignment

7. Databases URL: www.ncbi.nlm.nih.gov URL: www.rcsb.org
Sequence Database
Structural Database

8. Repository
URL:

9. Formats of sequence writing:
FastP  used previously for protein sequences
FastN used previously for nucleotide sequences
FastA  most common and recent format used for both protein and nucleotide sequences.
FASTA format
>ATCCATGCGCGATGCATGGTCATG
>gi| |HsHbA
ATCCTAGCATCCGGATATGGCATA
GenBank format

10. Sequence Alignment SEQ 1: AATTAAT SEQ 2: ATTTTAT Score = 5 Score = 2
SEQ 1: ATTGCATAA
SEQ 2: ATGCTTAGC
Score = 2

11. Gap introduction (gi) and Gap Extensions (gex)
Alignment using Gaps
SEQ 1: ATTGCATAA ATTGCATAA SEQ 2: ATGCTTAG A-TGCTTAG
Gap introduction (gi) and Gap Extensions (gex)
SEQ 3: GCATGCGCTAA GCATGCGCTAA
SEQ 4: GATTAA G-AT----TAA gi
gex

12. However, gapped matches might not always be desirable.
Gap Penalty (Gp):
Gp = gi + gex
Score(s) = S – Gp
Amino acid substitution matrices
BLOSUM (Block Substitution Matrix)
PAM (Accepted Point Mutation)

15. Quantifying alignment results
P-value: The P-value of an identified similarity of Score S is the probability that a score of atleast S (i.e., S or greater than S) would have been obtained in a chance match between two unrelated sequences of similar composition and length.
E-value: For an identified similarity of score S the E-value is the expected frequency of scores of atleast S. (It is the number of scores of atleast S that would have been expected to have occurred by chance.)

16. Sequence alignment types
Pair – wise alignment
Here one sequence is aligned with another sequence.
Two types -
Local alignment
Global alignment
Multiple sequence alignment
Here more than two sequences are aligned with each other.

17. Global alignment Local alignment
SEQ 1:
ATGCATGCATCGTAGC
ATGCATGGCATGTAGT
SEQ 2:
Complete sequence is aligned.
Smallest information is not obtained.
In case of ancestral study or phylogenetic study global alignment is more predictable.
SEQ 1:
ATGCATGCATCGTAGC
TATGTCGCATTCATCT
SEQ 3:
A part of the sequence is aligned.
Smallest information is obtained.
It is not preferred in case of ancestral study or phylogenetic study.

18. National Center for Biotechnology Information

19. Basic Local Alignment Search Tool (BLAST)

21. Next class on Multiple sequence alignment