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Micro 6th Sem Paper 2 Notes, by Adarsh Kamal

The document provides an overview of computers, including their definitions, types based on mechanism, size, and purpose, as well as the generations of computers and programming languages. It categorizes computers into analog, digital, and hybrid types, and discusses various sizes from supercomputers to microcomputers. Additionally, it explains low, medium, and high-level programming languages, along with types of computer memory such as primary, secondary, and cache memory.

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0% found this document useful (0 votes)
9 views12 pages

Micro 6th Sem Paper 2 Notes, by Adarsh Kamal

The document provides an overview of computers, including their definitions, types based on mechanism, size, and purpose, as well as the generations of computers and programming languages. It categorizes computers into analog, digital, and hybrid types, and discusses various sizes from supercomputers to microcomputers. Additionally, it explains low, medium, and high-level programming languages, along with types of computer memory such as primary, secondary, and cache memory.

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adarshkamal233
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© © All Rights Reserved
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UNIT : 1 INTRODUCTION TO

COMPUTERS
Computer
The ter mcomputer r efers to an el ectr onic device that is capabl e of r eceiving input, pr ocessing data accor ding to a
set of instr uctions (cal l ed a pr ogram), and pr oducing output or stor ing the r esults.
In simpl e ter ms, a computer is a machine that per for ms cal cul ations, pr ocesses infor mation, and automates tasks
using har dwar e (physical components) and softwar e (pr ograms and operating systems).

1. Based on Mechanism
(i). Anal og Computers: These computers pr ocess continuous data, such as physical quantities l ike temperatur e,
pr essur e, and voltage. They ar e often used in scientif ic and industr ial appl ications. Eg, Anal og cl ocks (measur e
time continuously), Anal og cl ocks (measur e time continuously).

(ii). Digital Computers: The most common type today, they pr ocess discr ete data in the for mof binar y digits (0s and
1s). Exampl e: Most moder n computers, incl uding personal computers, l aptops, and smar tphones, ar e digital
computers.

(iii). Hybr id Computers: Combine featur es of both anal og and digital computers. They can pr ocess both continuous
and discr ete data and ar e used in special ized appl ications. Exampl e: ECG machines (anal og
sensors + digital displ ay). Petr ol pump meters (measur e fuel f l ow anal og + digital pr ice cal cul ation).

2. Based on size
(i). Super computers: The most power ful and expensive type of computer , capabl e of per for ming tr il l ions of
cal cul ations per second. They ar e used for compl ex tasks l ike weather for ecasting, scientif ic r esear ch, and
simul ations.eg. Fr ontier (USA) –Fastest super computer (2023), Fugaku (Japan) –For mer #1, used for COVID
r esear ch, IBM Summit –Used in cl imate model ing.

(ii). Mainframe Computers: Lar ge, power ful computers used by or ganizations to pr ocess huge amounts of data, such
as in banking, insurance, and gover nment sectors. They can handl e numer ous users simultaneously. Exampl e: IBM's
zSer ies mainframes ar e used by many l ar ge or ganizations. They ar e about the size of a smal l r oom's cabinet. They
can handl e thousands of transactions per second and have a l ar ge number of input/output channel s to connect to
var ious per ipheral devices and networ ks.

(iii). Minicomputers (Mid- range Ser vers): These ar e smal l er and l ess power ful than mainframes but stil l capabl e of
suppor ting multipl e users. They ar e used in smal l er or ganizations and for specif ic tasks l ike industr ial pr ocess
contr ol . Exampl e: The PDP - 11ser ies of minicomputers was a popul ar type. It was used in industr ial contr ol
systems.
(iv). Micr ocomputers or Personal Computers (PCs)
It was intr oduced in 1970. It can suppor t one user at a time. Micr o computer ar e the smal l estcomputer system.
Ther e size range fr omcal cul ator to desktop size. It is typical ly singl e CPU, singl e usinsystemwhich is used at
home, school s, shops etc.
Exampl es - . Desktop PCs –For off ice/home use (Del l OptiPl ex).
Laptops –Por tabl e (MacBook Pr o, HP Pavil ion).
Tabl ets –Touchscr een (iPad, Micr osoft Sur face).
Smar tphones –Advanced mobil e computing (iPhone, Andr oid).
3. Based on Purpose
(i). General - Pur pose Computers: Designed to per for ma wide var iety of tasks, such as personal computers used for
wor d pr ocessing, web br owsing, and gaming. OR These computers ar e designed to handl e a wide var iety of tasks. They
can per for mdiffer ent functions by instal l ing differ ent softwar e. Their har dwar e ar chitectur e is f l exibl e and can adapt
to var ious appl ications. Exampl e. A typical personal computer is a general - pur pose computer . You can use it for
wr iting documents using wor d pr ocessing softwar e, editing photos with image - editing softwar e, br owsing the inter net,
and even pl aying games by instal l ing the appr opr iate game softwar e.

(ii). Special - Pur pose Computers: Designed for a specif ic task, such as computers in automobil es, micr owave ovens, and
industr ial contr ol systems (al so known as embedded computers). OR These computers ar e designed for a specif ic task or
a nar r ow range of tasks. Exampl e: Automatic tel l er machines (ATMs) ar e special - pur pose computers. Their pr imar y
function is to handl e bank car d transactions such as withdrawal s and bal ance inquir ies.

# Computer Generations
1. First Generation (1940–1956): VacuumTubes
Technol ogy Used: Vacuumtubes for cir cuitr y, magnetic dr ums for memor y.
Pr ogramming Language: Machine l anguage (binar y code).
Character istics:
Lar ge and bul ky machines.
High el ectr icity consumption and heat pr oduction.
Sl ow pr ocessing speed and l ow r el iabil ity.
Exampl es: ENIAC, UNIVAC.

2. Second Generation (1956–1963): Transistors


Technol ogy Used: Transistors r epl aced vacuumtubes.
Pr ogramming Language: Assembly l anguage, ear ly high- l evel l anguages l ike FORTRAN and COBOL.
Character istics:
Smal l er , faster , mor e r el iabl e, and mor e ener gy- eff icient than f irst- generation computers.
Stil l expensive and used mainly by gover nments and l ar ge or ganizations.
Exampl es: IBM 1401, IBM 7090.
3. Thir d Generation (1964–1971): Integrated Cir cuits (ICs)
Technol ogy Used: Integrated Cir cuits instead of individual transistors.
Pr ogramming Language: High- l evel l anguages became common (e.g., BASIC, PASCAL).
Character istics:
Even smal l er and mor e power ful .
Mor e affor dabl e, al l owing br oader commer cial use.
Intr oduced operating systems for better r esour ce management.
Exampl es: IBM System/360, PDP- 8.

4. Four th Generation (1971–Pr esent): Micr opr ocessors


Technol ogy Used: Micr opr ocessors (thousands of ICs on a singl e chip).
Pr ogramming Language: Advanced high- l evel l anguages (C, C++, Java).
Character istics:
Emer gence of personal computers (PCs).
Graphical User Inter face (GUI) devel opment.
Networ king and the inter net.
Exampl es: Intel 4004, IBM PC, Appl e Macintosh.

5. Fifth Generation (Pr esent and Beyond): Ar tif icial Intel l igence (AI)
Technol ogy Used: Based on AI, machine l ear ning, quantumcomputing, and paral l el pr ocessing.
Pr ogramming Language: AI- specif ic l anguages (e.g., Python, Pr ol og, LISP).
Character istics:
Focus on smar t systems that can l ear n and make decisions.
Natural Language Pr ocessing, Robotics, Exper t Systems.
Stil l evolving, with appl ications in autonomous vehicl es, chatbots, etc.
# Pr ogramming l anguages
A pr ogramming l anguage is a way for peopl e to give instr uctions to a computer . It uses special wor ds and r ul es to
cr eate pr ograms that tel l the computer what to do.

(i). Low Level Pr ogramming Languages


A l ow- l evel pr ogramming l anguage dir ectly instr ucts the computer , usual ly in binar y, decimal , or hexadecimal
for m. Low- l evel pr ogramming l anguages, l ike machine code or assembly l anguage, ar e diff icult for humans to
r ead and compr ehend. Ever y command given to the computer has to be compl etely wr itten out.

Types of Low- Level Languages - Low l evel l anguage ar e divided into two types.

Machine Language
We know that machines fol l ow the l anguage of binar y system, means 0 and 1. Machine l anguage is l ow l evel
l anguage which consists of binar y codes which ar e dir ectly operated by CPU Central Pr ocessing Unit. Ther e ever y
instr uction ar e wr itten in for mof 0 and 1, so its ver y chal l enging for humans to understand and use as pr imar y
l anguage.

Assembly Language
Assembly Language is a way of wr iting computer pr ograms that ar e ver y cl ose to how the computer wor ks. It have
some symbol s and codes that r epr esent the basic operations that the computer can per for m, which incl udes
adding, moving, or compar ing numbers. Because ever y computer use differ ent ar chitectur e for pr ocessing so
computer have ther e own instr uctions so we can say ever y computer have ther e own assembly l anguage. It is way
higher l evel l anguage then machine l anguage so its mor e faster and but stil l its har d to wr ite and r ead. To r un a
pr ogramwr itten using assembly l anguage we need to conver t it to machine l anguage which is binar y . This
conversion is done by a pr ogramcal l ed an assembl er .

(ii). Medium Level Pr ogramming Languages


Middl e- l evel l anguage is a computer l anguage in which the instr uctions ar e cr eated using symbol s such as
l etters, digits and special characters. Assembly l anguage is an exampl e of middl e- l evel l anguage. In assembly
l anguage, we use pr edef ined wor ds cal l ed mnemonics. Binar y code instr uctions in l ow- l evel l anguage ar e r epl aced
with mnemonics and operands in middl e- l evel l anguage. But the computer cannot understand mnemonics, so we use
a transl ator cal l ed Assembl er to transl ate mnemonics into binar y l anguage. Assembl er is a transl ator which
takes assembly code as input and pr oduces machine code as output. That means, the computer cannot understand
middl e- l evel l anguage, so it needs to be transl ated into a l ow- l evel l anguage to make it understandabl e by the
computer . Assembl er is used to transl ate middl e- l evel l anguage into l ow- l evel l anguage. C l anguage can be used
to wr ite both systemsoftwar e and appl ication softwar e.
Advantages.
Wr iting instr uctions in a middl e- l evel l anguage is easier than wr iting instr uctions in a l ow- l evel l anguage..
Middl e- l evel l anguage is mor e r eadabl e compar ed to l ow- l evel l anguage.. Easy to understand, f ind er r ors and
modify.
Disadvantages. Middl e- l evel l anguage is specif ic to a par ticul ar machine ar chitectur e, that means it is machine-
dependent.. Middl e- l evel l anguage needs to be transl ated into l ow- l evel l anguage.. Middl e- l evel l anguage
executes sl ower compar ed to l ow- l evel l anguage. OR
Medium- l evel l anguages br idge the gap between the high- l evel abstraction of human- l ike l anguages and the l ow-
l evel contr ol of machine code. It is a computer l anguage which makes use of symbol s such as l etters, digits and
special characters to cr eate instr uctions. An exampl e of Medium- l evel l anguage is Assembly l anguage. In an
assembly l anguage, pr edef ined wor ds cal l ed mnemonics ar e used. Other medium- l evel l anguages ar e C and C++.
(iii). High Level Pr ogramming Languages
A high- l evel l anguage is a computer l anguage which can be understood by the users. The high- l evel l anguage is
ver y simil ar to human l anguages with set of r ul es that ar e used to make instr uctions mor e easily. Ever y high-
l evel l anguage has a set of pr edef ined wor ds known as Keywor ds and a set of r ul es known as Syntax to cr eate
instr uctions.The high- l evel l anguage is easier to understand for the users but the computer can not understand
it.. High- l evel l anguage needs to be conver ted into the l ow- l evel l anguage to make it understandabl e by the
computer .. We use Compil er or inter pr eter to conver t high- l evel l anguage to l ow- l evel l anguage.
High l evel l anguages l ike COBOL, Pascal , Python , Java and others enabl e the pr ogrammer to wr ite codes that
ar e mor e or l ess independent of a par ticul ar type of computer .
Advantages
High- l evel l anguages ar e user - fr iendly, as they use simpl e Engl ish- l ike syntax, making themeasier to l ear n and
wr ite. They ar e al so por tabl e, meaning code can r un on differ ent pl atfor ms with minimal modif ications.
Additional ly, they automate memor y management and compl ex operations, r educing devel opment time and
er r ors.
Disadvantages
They ar e sl ower than l ow- l evel l anguages because they r equir e transl ation (compil ation/inter pr etation) into
machine code. They al so offer l ess contr ol over har dwar e, making themunsuitabl e for tasks r equir ing pr ecise
systemmanipul ation, such as embedded systems or r eal - time appl ications.

Types of Computer Memory


In general , computer memor y is divided into thr ee types:
Pr imar y memor y, Secondar y memor y and Cache memor y

1. Primary Memory/Main Memory/Internal Memory


It is al so known as the main memor y of the computer system. It is used to stor e data and pr ograms or instr uctions
dur ing computer operations. It uses semiconductor technol ogy and hence is commonly cal l ed semiconductor
memor y. Pr imar y memor y is of two types:
RAM (RandomAccess Memor y): It is a vol atil e memor y. Vol atil e memor y stor es infor mation based on the power
supply. If the power supply fail s/ inter r upted/stopped, al l the data and infor mation on this memor y wil l be l ost.
RAM is used for booting up or star ting the computer . It temporar ily stor es pr ograms/data which has to be
executed by the pr ocessor . RAM is of two types:

S RAM (Static RAM): S RAM uses transistors and the cir cuits of this memor y ar e capabl e of r etaining
their state as l ong as the power is appl ied. This memor y consists of the number of f l ip f l ops with each
f l ip f l op stor ing 1bit. It has l ess access time and hence, it is faster .
D RAM (Dynamic RAM): D RAM uses capacitors and transistors and stor es the data as a char ge on the
capacitors. They contain thousands of memor y cel l s. It needs r efr eshing of char ge on capacitor after a
few mil l iseconds. This memor y is sl ower than S RAM.
ROM (Read Only Memor y): It is a non- vol atil e memor y. Non- vol atil e memor y stor es infor mation even when ther e
is a power supply fail ed/ inter r upted/stopped. ROM is used to stor e infor mation that is used to operate the
system. As its name r efers to r ead- only memor y, we can only r ead the pr ograms and data that ar e stor ed on it.
It contains some el ectr onic fuses that can be pr ogrammed for a piece of specif ic infor mation. The infor mation
is stor ed in the ROM in binar y for mat. It is al so known as per manent memor y. ROM is of four types:

MROM(Masked ROM): Har d- wir ed devices with a pr e- pr ogrammed col l ection of data or instr uctions
wer e the f irst ROMs. Masked ROMs ar e a type of l ow- cost ROM that wor ks in this way.
PROM (Pr ogrammabl e Read Only Memor y): This r ead- only memor y is modif iabl e once by the user . The
user pur chases a bl ank PROM and uses a PROM pr ogramto put the r equir ed contents into the PROM.
Its content can't be erased once wr itten.
EPROM (Erasabl e Pr ogrammabl e Read Only Memor y): EPROM is an extension to PROM wher e you can
erase the content of ROM by exposing it to Ultraviol et rays for near ly 40 minutes.
EEPROM (El ectr ical ly Erasabl e Pr ogrammabl e Read Only Memor y): Her e the wr itten contents can be
erased el ectr ical ly. You can del ete and r epr ogramEEPROM up to 10, 000 times. Erasing and
pr ogramming take ver y l ittl e time, i.e., near ly 4 - 10 ms(mil l iseconds). Any ar ea in an EEPROM can be
wiped and pr ogrammed sel ectively.

2. Secondary Memory/Secondary Storage Devices


It is al so known as auxil iar y memor y and backup memor y. It is a non- vol atil e memor y and used to stor e a l ar ge
amount of data or infor mation. The data or infor mation stor ed in secondar y memor y is per manent, and it is
sl ower than pr imar y memor y. A CPU cannot access secondar y memor y dir ectly. The data/infor mation fr omthe
auxil iar y memor y is f irst transfer r ed to the main memor y, and then the CPU can access it.
Character istics of Secondar y Memor y
It is a sl ow memor y but r eusabl e.
It is a r el iabl e and non- vol atil e memor y.
It is cheaper than pr imar y memor y.
The storage capacity of secondar y memor y is l ar ge.
A computer systemcan r un without secondar y memor y.
In secondar y memor y, data is stor ed per manently even when the power is off .
Types of Secondar y Memor y
1. Magnetic Tapes: Magnetic tape is a l ong, nar r ow str ip of pl astic f il mwith a thin, magnetic coating on it that
is used for magnetic r ecor ding. Bits ar e r ecor ded on tape as magnetic patches cal l ed RECORDS that r un al ong
many tracks. Typical ly, 7 or 9 bits ar e r ecor ded concur r ently. Each track has one r ead/wr ite head, which
al l ows data to be r ecor ded and r ead as a sequence of characters. It can be stopped, star ted moving for war d or
backwar ds or r ewound.
2. Magnetic Disks: A magnetic disk is a cir cul ar metal or a pl astic pl ate and these pl ates ar e coated with
magnetic mater ial . The disc is used on both sides. Bits ar e stor ed in magnetized sur faces in l ocations cal l ed
tracks that r un in concentr ic r ings. Sectors ar e typical ly used to br eak tracks into pieces.
Har d discs ar e discs that ar e per manently attached and cannot be r emoved by a singl e user .
3. Optical Disks: It's a l aser - based storage mediumthat can be wr itten to and r ead. It is r easonably pr iced and
has a l ong l ifespan. The optical disc can be taken out of the computer by occasional users.
Types of Optical Disks
CD - ROM
It's cal l ed a compact disk. Only r ead fr ommemor y.
Infor mation is wr itten to the disc by using a contr ol l ed l aser beamto bur n pits on the disc sur face.
It has a highly r ef l ecting sur face, which is usual ly al uminium.
The diameter of the disc is 5.25 inches.
16000 tracks per inch is the track density.
The capacity of a CD- ROM is 600 MB, with each sector stor ing 2048 bytes of data.
The data transfer rate is about 4800KB/sec. & the new access time is ar ound 80 mil l iseconds.
WORM- (WRITE ONCE READ MANY)
A user can only wr ite data once.
The infor mation is wr itten on the disc using a l aser beam.
It is possibl e to r ead the wr itten data as many times as desir ed.
They keep l asting r ecor ds of infor mation but access time is high.
It is possibl e to r ewr ite updated or new data to another par t of the disc.
Data that has al r eady been wr itten cannot be changed.
Usual size - 5.25 inch or 3.5 inch diameter .
The usual capacity of a 5.25- inch disk is 650 MB, 5.2GB etc.
DVDs
The ter m"DVD" stands for "Digital Versatil e/Video Disc, " and ther e ar e two sor ts of DVDs:
DVDR (wr itabl e)
DVDRW (Re- Wr itabl e)
DVD- ROMS (Digital Versatil e Discs): These ar e r ead- only memor y (ROM) discs that can be used in a var iety of ways.
When compar ed to CD- ROMs, they can stor e a l ot mor e data. It has a thick polycar bonate pl astic l ayer that ser ves
as a foundation for the other l ayers. It's an optical memor y that can r ead and wr ite data.
DVD- R: DVD- R is a wr itabl e optical disc that can be used j ust once. It's a DVD that can be r ecor ded. It's a l ot l ike
WORM. DVD- ROMs have capacities ranging fr om4.7 to 17 GB. The capacity of 3.5 inch disk is 1.3 GB.
3. Cache Memory
It is a type of high- speed semiconductor memor y that can hel p the CPU r un faster . Between the CPU and the main
memor y, it ser ves as a buffer . It is used to stor e the data and pr ograms that the CPU uses the most fr equently.
Advantages of Cache Memor y
It is faster than the main memor y.
When compar ed to the main memor y, it takes l ess time to access it.
It keeps the pr ograms that can be r un in a shor t amount of time.
It stor es data for temporar y use.
Disadvantages of Cache Memor y
Because of the semiconductors used, it is ver y expensive.
The size of the cache (amount of data it can stor e) is usual ly smal l .

# DATA REPRESENTATION IN COMPUTERS


Data r epr esentation is how infor mation is encoded in a for mthat computers can inter pr et and pr ocess.
(a). Binar y Number System
The most fundamental r epr esentation: only two digits — 0 and 1.
Al l data, r egar dl ess of type, is ultimately conver ted into binar y.

(b). Repr esenting Differ ent Types of Data

Data Type Representat ion Example


Numbers Binary, Decimal - Binary conversion 5 0101
Text Character encoding systems "A“ 01000001(ASCII)
Images
# DATA STORAGE IN COMPUTERS Pixel val ues (RGB) encoded in binary JPEG, PNG
Audio Digital sampl ing of sound waves MP3, WAV
Video Sequence of image frames + audio MP4, AVI
Data storage is the pr ocess of saving digital data on physical or vir tual devices for cur r ent or futur e use.
(a). Storage Types

Storage Type Example Characterist ics


Fast, volat ile (RAM), essent ial for
Primary Storage RAM, ROM act ive tasks
Secondary Storage HDD, SSD Permanent, large capacity
(b.) Storage Units
Tert iary Storage Opt ical disks, tapes Used for backups, slower access
1Bit = SmalCloud
l est unit (0 or 1)
Storage Google Drive, iCloud Remote access, scalable
1Byte = 8 Bits
1KB = 1024 Bytes
1MB = 1024 KB
1GB = 1024 MB
1TB = 1024 GB
Unit 2 : Microsoft Excel
Aggr egate Functions in MS Excel
Aggr egate functions in Micr osoft Excel ar e built- in for mul as used to summar ize or analyze l ar ge amounts of
data. They per for mcal cul ations such as sum, average, count, max, min, etc., and ar e especial ly useful when
wor king with tabl es or data sets.

Some common Aggr egate Functions

Function Descr iption Exampl e


SUM() Adds al l the val ues =SUM(A1:A5)
AVERAGE() Cal cul ates the mean =AVERAGE(B1:B5)
MAX() Finds the l argest val ue =MAX(C1:C5)
MIN() Finds the smal l est val ue =MIN(C1:C5)
COUNT() Counts numeric val ues only =COUNT(A1:A10)
COUNTA() Counts non- empty cel l s (text + =COUNTA(A1:A10)
numbers)
COUNTBLANK() Counts empty cel l s =COUNTBLANK(A1:A10)
PRODUCT() Multipl ies val ues =PRODUCT(A1:A3)
MEDIAN() Finds the middl e val ue =MEDIAN(A1:A5)
Unit 3: Bioinformat ics

# BIOINFORMATICS
Bioinfor matics is an inter discipl inar y f iel d that mer ges biol ogy, computer science, mathematics, and infor mation
technol ogy to analyze and inter pr et biol ogical data. It pl ays a pivotal r ol e in managing and util izing the massive
amount of data generated by genomic, pr oteomic, and metabol omic r esear ch. The pr imar y aimof bioinfor matics is to
understand biol ogical pr ocesses thr ough computational model s and tool s, facil itating discover ies in ar eas such as
genomics, mol ecul ar biol ogy, and evol utionar y biol ogy.

Overview of Bioinformatics
At its cor e, bioinfor matics involves the devel opment and appl ication of computational tool s and al gor ithms to:
Col l ect and Stor e Biol ogical Data: This incl udes DNA, RNA, and pr otein sequences, gene expr ession data, pr otein
str uctur es, and other biol ogical infor mation. Databases l ike GenBank, Ensembl , and UniPr ot ar e central to this
function.
Analyze Biol ogical Data: Bioinfor maticians use sophisticated al gor ithms and statistical methods to extract meaningful
insights fr omraw biol ogical data. This involves tasks such as:
Sequence al ignment: Compar ing DNA, RNA, or pr otein sequences to identify simil ar ities and differ ences,
which can r eveal evol utionar y r el ationships or functional conser ved r egions.
Genome assembly and annotation: Reconstr ucting entir e genomes fr omfragmented sequencing r eads and
identifying genes, r egul ator y el ements, and other featur es.
Gene expr ession analysis: Studying how genes ar e tur ned on or off under differ ent conditions, pr oviding
insights into biol ogical pr ocesses and disease mechanisms.
Pr otein str uctur e pr ediction: Pr edicting the 3D str uctur e of pr oteins fr omtheir amino acid sequences, which
is cr ucial for understanding their function and designing dr ugs.
Phyl ogenetic analysis: Reconstr ucting evol utionar y r el ationships between or ganisms based on their genetic
data.
Disseminate Biol ogical Infor mation: Making analyzed data and tool s accessibl e to the wider scientif ic community
thr ough databases, web ser vers, and softwar e packages.
Scope:
The scope of bioinfor matics is vast and continual ly expanding with technol ogical advancements in high- thr oughput
sequencing and computational power . Maj or ar eas incl ude:
Biomedical Resear ch: Bioinfor matics hel ps identify disease- associated genes, pr edict dr ug tar gets, and devel op
personal ized medicine strategies.
Agr icultural Biotechnol ogy: It assists in cr op impr ovement, identif ication of genes r esponsibl e for str ess r esistance,
and devel opment of genetical ly modif ied or ganisms (GMOs).
Phar maceutical Devel opment: Used in dr ug discover y, vaccine design, and understanding dr ug interactions.
Envir onmental Bioinfor matics: Analysis of micr obial communities in differ ent envir onments for appl ications in waste
tr eatment, pol l ution contr ol , and bioener gy.
Comparative Genomics: Hel ps understand evol utionar y r el ationships and functions by compar ing genetic mater ial
acr oss species.
Machine Lear ning and AI Integration: Pr edictive model ing, patter n r ecognition, and diagnostic tool s in healthcar e ar e
incr easingly using AI- based bioinfor matics.

# GENOMICS
Genomics is the study of a person’s compl ete set of genes, and their interaction with each other and the envir onment.
Genomics is a foundational f iel d in moder n biol ogy that focuses on the compr ehensive study of an or ganism's genome—
the compl ete set of DNA, incl uding al l its genes and other functional el ements. Unl ike traditional genetics, which
often focuses on individual genes and their inher itance patter ns, genomics takes a hol istic appr oach, examining the
entir e genetic bl uepr int and how its components interact.
Scope and Appl ications:
Medical Genomics (Personal ized Medicine):
Genomics is transfor ming healthcar e by enabl ing personal ized tr eatment pl ans based on individual genetic pr of il es,
identifying disease r isk factors, and guiding gene therapy devel opment.
Cancer Genomics:
Hel ps identify mutations r esponsibl e for differ ent cancers, enabl ing tar geted therapy and ear ly diagnosis.
Agr icultural Genomics:
Used to enhance cr op yiel d, disease r esistance, and str ess tol erance thr ough mar ker - assisted br eeding and genetic
engineer ing.
Evol utionar y Biol ogy:
Pr ovides insights into speciation, adaptation, and the evol utionar y histor y of or ganisms by compar ing genomic sequences.
Infectious Disease Resear ch:
Hel ps trace pathogen evol ution, study antimicr obial r esistance, and devel op vaccines and diagnostics.
For ensics and Ancestr y:
Genomic data aids in cr iminal investigations and tracing l ineage and migration patter ns in popul ations.

# TRANSCRIPTOMICS
Transcr iptomics is the study of the compl ete set of RNA transcr ipts pr oduced by the genome under specif ic conditions
or in a par ticul ar cel l or tissue. This incl udes messenger RNA (mRNA), r ibosomal RNA (rRNA), transfer RNA (tRNA),
and non- coding RNAs. It is used to understand which genes ar e active (expr essed), when, wher e, and how much they ar e
expr essed.
Appl ications:
Identifying gene expr ession patter ns in diseases l ike cancer , Understanding how cel l s r espond to str ess, dr ugs, or
pathogens, Discover ing biomar kers for diagnostics

# PROTEOMICS
Pr oteomics is the study of the entir e set of pr oteins (pr oteome) pr oduced by a cel l , tissue, or or ganism. It is used to
understand pr otein str uctur e, function, interactions, and how pr oteins change under differ ent conditions.
Appl ications:
Dr ug tar get identif ication, Understanding disease mechanisms, Studying post- transl ational modif ications (e.g.,
phosphor yl ation)

# METABOLOMICS
Metabol omics is the study of the compl ete set of smal l mol ecul es (metabol ites) involved in metabol ismwithin a
biol ogical sampl e. It is used to analyze metabol ic changes and pathways active in a cel l or or ganismunder specif ic
conditions.
Appl ications:
Identifying metabol ic disor ders, Studying nutr ition and the effects of diet, Monitor ing dr ug effects and toxicity

# PROGRAMMING LANGUAGES IN BIOINFORMATICS


(i). Python
Python is one of the most widely used pr ogramming l anguages in bioinfor matics due to its simpl icity, r eadabil ity, and
vast col l ection of l ibrar ies. It is ideal for beginners and pr ofessional s al ike. Python is highly effective for tasks such
as sequence analysis, data visual ization, and automation. Popul ar l ibrar ies l ike Biopython pr ovide r eady- made functions
for wor king with DNA, RNA, and pr otein sequences, whil e NumPy and Pandas suppor t numer ical and tabul ar data
analysis. For visual ization, tool s l ike Matpl otl ib and Seabor n ar e widely used. Python is commonly used for scr ipting
pipel ines, handl ing biol ogical f il e for mats (l ike FASTA and GenBank), and integrating machine l ear ning in biol ogical
r esear ch.
(ii). R
R is a power ful l anguage mainly used for statistical computing and data visual ization, making it par ticul ar ly val uabl e in
bioinfor matics ar eas such as genomics, transcr iptomics, and epidemiol ogy. It is the pr efer r ed l anguage when deal ing
with l ar ge- scal e biol ogical datasets and per for ming statistical tests. The Bioconductor pr oj ect offers hundr eds of R
packages designed specif ical ly for bioinfor matics, incl uding tool s for analyzing gene expr ession data (l ike DESeq2 and
edgeR). R al so excel s in pr oducing high- qual ity graphs and pl ots with packages l ike ggpl ot2, making it essential for
data pr esentation and publ ication- r eady f igur es.
(iii). Per l
Per l was one of the f irst l anguages extensively used in bioinfor matics, known for its str ength in text pr ocessing and
r egul ar expr essions. Although its popul ar ity has decl ined in r ecent years, many l egacy systems and bioinfor matics
scr ipts ar e stil l wr itten in Per l . The BioPer l l ibrar y offers a suite of modul es for parsing and analyzing sequence
data, f il e for mats, and genomic featur es. Per l is par ticul ar ly useful for cr eating quick scr ipts to handl e biol ogical
text f il es and for manipul ating l ar ge vol umes of unstr uctur ed data, such as output fr omsequencing machines.
(iv). Java
Java is a r obust, obj ect- or iented l anguage known for buil ding compl ex, pl atfor m- independent bioinfor matics
appl ications with graphical user inter faces. Whil e not as common for data analysis tasks as Python or R, Java is used
in the devel opment of l ar ge- scal e softwar e systems l ike Taver na, MEGA, and the Integrative Genomics Viewer (IGV).
The Bio Java l ibrar y pr ovides tool s for pr ocessing sequence data, pr otein str uctur es, and mol ecul ar biol ogy
computations. Java’s str ength l ies in its scal abil ity, per for mance, and abil ity to cr eate user - fr iendly softwar e.
(v). C and C++
C and C++ ar e l ow- l evel , compil ed pr ogramming l anguages that offer high per for mance and memor y eff iciency, making
themideal for cr eating fast and r esour ce- intensive bioinfor matics tool s. Many foundational pr ograms l ike BLAST,
Bowtie, and SAMtool s ar e wr itten in C/C++ because they can handl e massive genomic datasets quickly. These l anguages
ar e best suited for tasks that r equir e al gor ithmdevel opment, optimization, and pr ocessing of l ar ge biol ogical f il es or
al ignment data. However , they ar e har der to l ear n compar ed to high- l evel l anguages l ike Python or R.
Unit 4: Introduct ion to Biol ogical Database

In bioinfor matics, databases pl ay a cr ucial r ol e in stor ing, or ganizing, and pr oviding access to biol ogical data.
They can be categor ized into pr imar y, secondar y, and composite databases based on the natur e of the data they
stor e and how it is der ived. Her e's a detail ed expl anation of each type:

PRIMARY DATABASES
Pr imar y databases stor es the exper imental ly der ived biol ogical data dir ectly submitted by r esear chers. The data
in these databases is or iginal , unpr ocessed, and often minimal in annotation, acting as the fundamental sour ce for
subsequent analyses. Once an entr y is submitted and assigned an accession number , the data in pr imar y databases
is general ly not changed, for ming a stabl e par t of the scientif ic r ecor d.
Pur pose: The main pur pose of pr imar y databases is to ar chive and distr ibute raw biol ogical data, enabl ing
r esear chers to access the or iginal data for fur ther analysis and inter pr etation.

Exampl es:
GenBank: A compr ehensive genetic sequence database maintained by the National Center for Biotechnol ogy
Infor mation (NCBI). It contains a vast col l ection of DNA sequences submitted by r esear chers wor l dwide.
EMBL- Bank: The pr imar y nucl eotide sequence database in Eur ope, par t of a tr ipar tite col l aboration with GenBank
and DDBJ (DNA Data Bank of Japan).
DDBJ: The pr imar y nucl eotide sequence database in Japan, hol ding a l ar ge amount of genetic data fr omvar ious
or ganisms.

SECONDARY DATABASES
Secondar y databases ar e der ived fr ompr imar y databases thr ough pr ocesses such as annotation, curation, or
analysis. They pr ovide additional infor mation and insights by or ganizing and inter pr eting the raw data fr om
pr imar y sour ces. OR Secondar y databases (al so cal l ed der ived or curated databases) contain pr ocessed,
inter pr eted, or annotated data der ived fr ompr imar y databases.
Pur pose: Secondar y databases aimto enhance the understanding and usabil ity of biol ogical data by offer ing
curated and analyzed infor mation, hel ping r esear chers to identify patter ns, functions, and r el ationships within
the data.

Exampl es:
Pfam: A database of pr otein famil ies that identif ies and cl assif ies pr otein domains and famil ies thr ough sequence
simil ar ities and functional annotations.
KEGG (Kyoto Encycl opedia of Genes and Genomes): An integrated database r esour ce that combines genomic,
chemical , and systemic functional infor mation, par ticul ar ly useful for studying metabol ic pathways and gene
functions.
InterPr o: A r esour ce that pr ovides pr otein family and domain annotations by combining multipl e pr otein signatur e
databases into a singl e sear chabl e database.

COMPOSITE DATABASES
Composite databases integrate data fr ommultipl e pr imar y and secondar y databases, pr oviding a unif ied and
compr ehensive r esour ce for var ious types of biol ogical infor mation.
Pur pose: Composite databases ser ve as central ized r epositor ies that br ing together diverse biol ogical data,
enabl ing r esear chers to access and analyze infor mation fr omdiffer ent domains in a cohesive manner .
Exampl es:
NCBI Entr ez System: A col l ection of inter connected databases (incl uding GenBank, PubMed, Pr otein,
Nucl eotide, etc.) that al l ows users to sear ch and r etr ieve data fr ommultipl e sour ces simultaneously.
Ensembl : A database that pr ovides genome sequence data, gene annotations, and comparative analyses
for var ious species, integrating data fr ommultipl e pr imar y and secondar y sour ces.

1. Alignment Tools
A. BLAST (Basic Local Al ignment Sear ch Tool )
Pur pose: Finds r egions of l ocal simil ar ity between sequences.
Types:
bl astn –DNA vs DNA
bl astp –Pr otein vs pr otein
bl astx –Transl ated nucl eotide vs pr otein
Use Case: Identifying homol ogous sequences, infer r ing function, or checking for contamination.
Website: https://bl ast.ncbi.nl m.nih.gov

B. Cl ustal Omega
Pur pose: Multipl e sequence al ignment (MSA) of pr otein or nucl eotide sequences.
Used for : Constr ucting phyl ogenetic tr ees, f inding conser ved domains.
Str engths: Scal abl e for l ar ge datasets, accurate al ignments.
Website: https://www.ebi.ac.uk/Tool s/msa/cl ustal o/
C. MUSCLE & MAFFT
Pur pose: High- accuracy MSA tool s.
Used for : Comparative genomics, conser ved motif identif ication.
Str engths:
MUSCLE –Accuracy and speed
MAFFT –Fast and handl es l ar ge datasets wel l

2. Similarity Search & Mot if Discovery Tools


A. FASTA
Pur pose: Simil ar to BLAST but optimized differ ently.
Str engths: Good for nucl eotide and pr otein sear ches, sensitive for distant matches.
B. HMMER
Pur pose: Uses pr of il e Hidden Mar kov Model s to f ind sequence homol ogs.
Used for : Pr otein domain detection, r emote homol ogy.
Str engths: Ver y sensitive to subtl e sequence simil ar ities.
Website: http://hmmer .or g
C. MEME Suite
Pur pose: Discovers conser ved motifs in sequences.
Tool s Incl uded: MEME (motif discover y), MAST (motif sear ch), FIMO (f ind individual motif occur r ences)
Used for : Regul ator y sequence analysis, transcr iption factor binding site detection.
Website: http://meme- suite.or g

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