2. Bioinformatics represents a new, growing area of
science that uses computational approaches to
answer biological questions.
•Use computer technologies and statistical methods
•Manage and analyze a huge volume of biological data

3. Correlated subjects

4. Biology
Biochemistry
Molecular Biology
Microbiology
Genetic engineering
Mathematics
Statistics
Computer science.

5. Biological ProblemBiological Problem
Statistical/ Mathematical
Solution
Computer Program
Bioinformatics
Software/ Tools
Biological data
Result 3
Test Candidate Result
in Wet Lab
Final Solution with
Laboratory Proof
Final Solution with
Laboratory Proof
+
Result 2
Result 1
Approximate Result

7. Analyze huge volume of data
Don’t need expensive wet lab
Same research can be repeated many times
No adverse effect
Time saving

9. Understanding Sequence Formats

10. An example of a multiple sequence FASTA file
>SEQUENCE_1
MTEITAAMVKELRESTGAGMMDCKNALSETNGDFDKAVQLLREKGLGKAAK
KADRLAAEGVSVKVSDDFTIAAMRPSYLSYEDLDMTFVENEYKALVAELEKE
NEERRRLKDPNKPEHKQFASRKQLSDAILKEAEEKIKEELKAQGKPEKIWDNII
PGKMNSFIADNSQLDSKLTLMGQFYVMDDKKTVEQVIAEKEKEFGGKIKIVEF
ICFEVGEGLEKKTEDFAAEVAAQL
>SEQUENCE_2
SATVSEINSETDFVAKNDQFIALTKDTTAHIQSNSLQSVEELHSSTINGVKFEE
YLKSQIATIGENLVVRRFATLKAGANGVVNGYIHTNGRVGVVIAAACDSAEVA
SKSRDLLRQICMH
Fasta sequence always start with this sign
Fasta sequence will always have a sequence header

11. GenBank
gi|gi-number|gb|accession|locus
EMBL Data Library
gi|gi-number|emb|accession|locus
DDBJ, DNA Database of Japan
gi|gi-number|dbj|accession|locus
Sequence Header Example from Various Sequence Database
NBRF PIR
pir||entry P
Protein Research Foundation
prf||name
SWISS-PROT
sp|accession|name Brookhaven

12. Protein Data Bank
(1) pdb|entry|chain Brookhaven Protein Data Bank
(2) entry:chain|PDBID|CHAIN|SEQUENCE Patents pat|country|number
GenInfo Backbone
Id bbs|number
General database identifier
gnl|database|identifier
NCBI Reference Sequence
ref|accession|locus
Local Sequence identifier
lcl|identifier
Some More Example

13. Fasta File Extensions &Meaning

14. Extension Meaning Notes
fasta (.fas) generic fasta
Any generic fasta file. Other extensions
can be fa, seq, fsa
fna fasta nucleic acid Used to generically specify nucleic acids.
ffn FASTA nucleotide coding regions Contains coding regions for a genome.
faa fasta amino acid
Contains amino acids. A multiple protein
fasta file can have the more specific
extension mpfa.
frn FASTA non-coding RNA
Contains non-coding RNA regions for a
genome, in DNA alphabet e.g. tRNA,
rRNA
File extension
There is no standard file extension for a text file containing FASTA formatted sequences. The table
below shows each extension and its respective meaning.

15. Take a look to NCBI Nucleotide database

16. Uniprot Protein Database Showing Link to Download Sequence in Fasta Format