1 views

Uploaded by Keerthi Kalesan

Learn bioinfo

- AP Bio Genetics Question
- Strain Development 1
- Computer Evolution
- Additional Mathematics Project Work 1/2013 Selangor
- Curve Fitting
- tmp72B0
- General Mathematics Daily Lesson Log
- A level Mathematics Practice Paper F – Pure Mathematics mark scheme.docx
- AACR Report 2014
- Dave Thessis 2
- Genetics is Concerned With Explaining How Some Characteristics Are Passed
- 12. chapter 3.4.docx
- genomic research.pdf
- cycle 4 adv-algebra
- edwards unit plan
- ON A SERIES INVOLVING S(1) ·S(2) ... ·S(n)
- Answers 1st Assessment Mathematics for MEL 2015-2016
- Third Test
- Addmath Project Ref
- Financial marketing vol 1- Introduction and Essential Math

You are on page 1of 24

PAM-1?

Look at 71 groups of protein sequences

where the proteins in each group are at

least 85% similar (Why these groups?)

Compute relative mutability of each amino

acid probability of change

From relative mutability, compute

mutability probability for each amino acid

pair X,Y probability that X will change to Y

over a certain evolutionary time

Normalize the mutability probability for

each pair to a value between 0 and 1

the Likelihood that an Amino Acid Will Mutate

For each amino acid

Changes (p) = number of times the amino acid

changed into something else

exposure to mutation =

(percentage occurrence of the amino acid in the

group of sequences being analyzed) * (frequency of

amino acids changes in the group based on the

phylogenetic tree)

relative mutability =

(changes/exposure to mutation) / 100

Computing

Mutability Probability Between Amino Acid Pairs

r = relative mutability of X

c = num times X becomes Y or vice versa

p = num changes involving X

mutability probability of X to Y =

(r * c) / p

changes = # times A changes into something else = 4

% occurrence of A in group = 10 / 63 = 0.159

frequency of all amino acid changes in group = 6 * 2 = 12

(Note: Count changes backwards and forwards.)

exposure to mutation = (% occurrence of A in group)

* (frequency of all amino acid changes in group)

= 12 * 0.159

relative mutability = (changes / exposure to mutation) / 100

= (4 / (12 * 0.159)) = 2.09 / 100 = 0.0209

1 substitution per 100 residues.

Example from Fundamental Concepts of Bioinformatics by Krane

and Raymer.

A will change to G:

r = relative mutability of A = .0209

c = num times A becomes G or vice versa

=3

p = num changes involving A = 4

mutability probability of A to G =

(r * c) / p = (0.0209 * 3) / 4 = 0.0156

Normalizing

Mutability Probability, X to Y

For each Y among all amino acids,

compute mutability probability of X to Y

as described above

Get a total of these 20 probabilities.

Divide them by a normalizing factor such

that the probability that X will NOT

change is 99% and the sum of

probabilities that it will change to any

other amino acid is 1%

Converting

Mutability Probabilities to

Log Odds Score for X to Y

Y as follows:

Get the X to Y mutability probability

Divide by the % frequency of X in the sequence

data

Convert to log base 10, multiply by 10

log10(.098)

To compute log10(.098) solve for x:

10x = 0.098

x = -1.01

A score of 0 indicates that the change

from one amino acid to another is what is

expected by chance

A negative score means that the change is

probably due to chance

A positive score means that the change is

more than expected by chance

Because the scores are in log form, they

can be added (i.e., the chance that X will

change to Y and then Y to Z)

Disadvantages of PAM

Matrices

A

phylogenetic

tree

must

be

constructed

first,

implying

some

circularity in the analysis

Disadvantage:

The original PAM-1

matrix was based on a limited number

of

families,

not

necessarily

representative of all protein families

The Markov model does not take into

account that multi-step mutations

should be treated differently from

single-step ones

- AP Bio Genetics QuestionUploaded bySam Golden
- Strain Development 1Uploaded byolamicro
- Computer EvolutionUploaded bySean Pitman, MD
- Additional Mathematics Project Work 1/2013 SelangorUploaded byRichard Yii
- Curve FittingUploaded byCillalois Marie Famero
- tmp72B0Uploaded byFrontiers
- General Mathematics Daily Lesson LogUploaded byjun del rosario
- A level Mathematics Practice Paper F – Pure Mathematics mark scheme.docxUploaded byZaka Ahmed
- AACR Report 2014Uploaded byDonciu Alexandra
- Dave Thessis 2Uploaded byErik David Pilataxi Fernández
- Genetics is Concerned With Explaining How Some Characteristics Are PassedUploaded byitachi_93
- 12. chapter 3.4.docxUploaded byTang Bio
- genomic research.pdfUploaded byRoger Veramendi Fernandez
- cycle 4 adv-algebraUploaded byapi-262886009
- edwards unit planUploaded byapi-278223037
- ON A SERIES INVOLVING S(1) ·S(2) ... ·S(n)Uploaded byMia Amalia
- Answers 1st Assessment Mathematics for MEL 2015-2016Uploaded byAngela Aprina Kartika Putri
- Third TestUploaded byMiguel Anthony Rafanan
- Addmath Project RefUploaded byEdward Yee Kwan-Shuen
- Financial marketing vol 1- Introduction and Essential MathUploaded byPedro Porto
- exp_log_eqns_nUploaded byViet Quoc Hoang
- 3604264Uploaded byAldenilo Vieira
- Rev 1 - Algebra-exam - Set a - For Quizzers - Answer KeyUploaded byMarc Rivera
- SQL_PLSQLUploaded bykamalprabha
- SQL_PLSQLUploaded byDsp Chowdary
- evolutionunitstandardsUploaded byapi-300732604
- Lecture 14Uploaded byEric Parker
- Mechanisms of Evolutionary ChangeUploaded byShara Oliveros
- Science Glycerol 3Uploaded byIju Izzu
- On the F.Smarandache LCM function and its mean valueUploaded byMia Amalia

- Basic Energy TechniquesUploaded by李孟浩
- spectrum.pdfUploaded byKeerthi Kalesan
- Flora Sage Therapies Golden TrifectaUploaded byAishwarya Srivastava
- Auras - Sls Free GuidesUploaded byKeerthi Kalesan
- MuladharaUploaded byAndoni Silva
- upgmaUploaded byKeerthi Kalesan
- Learning DiaryUploaded byKeerthi Kalesan
- The Raven_s CallUploaded byKeerthi Kalesan
- Patch ClampUploaded byKeerthi Kalesan
- Phe and Cry PlantUploaded byKeerthi Kalesan
- ImpUploaded byKeerthi Kalesan
- Molecular Farming in PlantsUploaded byKeerthi Kalesan
- Quality Enhancement of CropsUploaded byKeerthi Kalesan
- Diploma 3Uploaded byKeerthi Kalesan

- Centrifugal CompressorsUploaded byKarim Ben
- Kogene Food SafetyUploaded byChandra Mohan Rajendran
- HighretortCPP a Easypeel (3)Uploaded byTrung Ho
- Git Version Control CertificationUploaded byVskills Certification
- bcom 314 task 4 - company narrativeUploaded byapi-453695036
- sarvesh samrat new project - Copy.docxUploaded byashwani
- Condenser Cycle TempoUploaded bykanggunkz
- Dynamic Stiffness Optimization Using RadiossUploaded byMounika Katragadda
- RMP2G 0007 SP 001 Structural Design Criteria Rev a 20110412Uploaded byAndrea Rusconi
- SMU contentsUploaded bySharath Kamath
- FundraisingUploaded byVladimir Josipović
- FTC Meticulously Dismantles Motion to Dissolve Injunction Against Don Juravin Personally and All DefendantsUploaded byJuro
- OTTcity WatergateUploaded bymitch9438
- SAS SUGI PaperUploaded bybiswarup1988
- audio listUploaded byapi-290759337
- Business LegislationUploaded byTrishana Jangral
- Anchor block and Thrust block Design and stability checkUploaded byEngr AtaUllah
- Getting Started With MASM and Visual Studio 2015Uploaded byHugo Betto Wilde Lunicer
- optical communicationUploaded byhemu70
- olpers.Uploaded bynavaal saeed
- AIR TESTUploaded byHarry Doble
- EKKO II - Digital RadarjammingUploaded byNick Numlk
- g Tower ReportUploaded byElaine Bong
- Limketkai Sons Milling v. CAUploaded byMykee Naval
- www.digitoly.com Complete Collection of Steve Jobs QuotesUploaded byKrishan Kant
- All PileUploaded byAstrid Aubry
- 8051 Micro Controller HistoryUploaded bytarakp_1
- abs-aflUploaded bymhofu
- PLC vs ControllerUploaded byththee
- Acceptance of Public DepositsUploaded bySukirti Shikha