Introduction to Bioinformatics Tuesday, 29 January

Introduction to BioinformaticsTuesday, 29 January

Can we push the due date to Friday?

X


Comments from Questionnaire

I need a textbook to teach me the basics.





I don't understand the purpose of mates.

I'm not really sure how to go about figuring out how much 1X of the

genome would be. How much what? Is this referring to nucleotides or contigs?

What is the purpose of a DNA library?

What do you do think is the better option for everyday sequencing

use in the real world: Dideoxy or shotgun genome?

Shotgun Sequence of a Genome

Drosophila genome(~100 million nt)

Shotgun Sequence of a Genome

Shotgun Sequence of a Book

Marley was dead, to begin with. There is no doubt whatever about that. The register of his burial was signed by the clergyman, the clerk, the undertaker, and the chief mourner. Scrooge signed it. And Scrooge's name was good upon 'Change for anything he chose to put his hand to.

Old Marley was as dead as a doornail.


Marley was dead, to begin with. There is no doubt whatever about that. The register of his burial was signed by the clergyman, the clerk, the undertaker, and the chief mourner. Scrooge signed it. And Scrooge's name was good upon 'Change for anything he chose to put his hand to.



Marley was

begin wit

dead, to be

ad, to begi

There is no doub

Marley was dead


…you would have to oversample a sequence for the shotgun

approach to work?

Sequencing processDrosophila genome(~100 million nt)

. . .Suppose broken into 500 nt fragments


. . .SAMPLE


SAMPLE

. . .

Marley was

begin wit

dead, to be

ad, to begi

There is no doub

Marley was dead

Marley was dead, to begin with. There is no doub


Marley was

begin wit

dead, to be

ad, to begi

There is no doub

Marley was dead



Marley was

begin wit

dead, to be

ad, to begi

There is no doub

Marley was dead

Marley was dead, to begin with.


There is no doub

Contig #47

Contig #29 How to connect contigs?How to get the snippets?

Dideoxy sequencingCGACCATCGCCTTAGTAC

DNA replication

DNA replication

DNA replication

DNA replication

Dideoxy sequencing

Dideoxy sequencing

Dideoxy sequencing

Dideoxy sequencing

Dideoxy sequencing

Dideoxy sequencing

Dideoxy sequencing

What is the sequence (5' to 3') represented by the gel? G A T C

Myers et al SQ2

What is the sequence (5' to 3') represented by the gel? G A T C

ddCddC

ddCddC

ddC

TCGTGTACATCGTAACACGGTTAAGT

Myers et al SQ2

Dideoxy sequencing

Study Question 4What is high-quality sequence?

G A T C


To determine high quality sequences,… How do you know when a peak stops

being high enough?

Could you explain in more detail the fluorescence chart

with the waves.


Dideoxy sequencingHow sure are you?

To determine high quality sequences,… How do you know when a peak stops

being high enough?

For SQ3, I have been unable to identify the organism/molecule by using

BioBIKE. I have tried the function SEQUENCES-SIMILAR-TO.

DNA replication

DNA replication

Primer

How to provide a primer to an

unknown sequence?

G A T Cprimer

primer

plasmid

insert

~2000 nt mates

Myers et al SQ6Why read pairs? Scaffolds?

What is the purpose of a DNA library?

primer

plasmid

insert~40 letters

Mate pairs

How to connect contigsWhy read pairs? Scaffolds?

dead, to begin with. There is no doub

. . .

~ 150,000 nt

Bacterial Artificial CHROMOSOME

mates

Myers et al SQ6Why read pairs? Scaffolds?

What is BAC used for again? .

I don't understand the purpose of mates.

Marley was dead. God bless us every one.

Marley was

begin wit

dead, to be

ad, to begi

There is no doub

Marley was dead

Marley was dead, to begin with.


There is no doub

Contig #47

Contig #29 How to connect contigs?

Marley was

begin wit

dead, to be

ad, to begi

There is no doub

Marley was dead



How are gaps between assembled contigs "closed experimentally"?

Marley was dead, to begin with. There is no doubt whatever

about that. The register of his burial was signed by the

clergyman, the clerk, the undertaker, and the chief mourner.

Scrooge signed it. And Scrooge's name was good upon

'Change for anything he chose to put his hand to.



Polymerase Chain Reaction (PCR)

Requires known primer sequences,one on each of the two strands.

with. Ther

Sequencing vs AssemblyDideoxy sequencing

G A T C GGGATATGTCAGACGGTA

AATACAAGAACCCAAGCACCCAATTAA

GTCCGATAGGCTCTTGTCG

TCTGGAAGCATTTAACCG

TAATTCTCTTTGTTATGGTGTCTGACC

TGCAGCGTCAGCGAAA

TAAATTCTGCTAGTGTCCGGTTTGC

CGGATACGCGCGAGAACTGACGACAACTCAGCGA

Sequence assembly

Contig 1 Contig 2

Finishing

Sequencing vs AssemblyDideoxy sequencing

G A T C GGGATATGTCAGACGGTA

AATACAAGAACCCAAGCACCCAATTAA

GTCCGATAGGCTCTTGTCG

TCTGGAAGCATTTAACCG

TAATTCTCTTTGTTATGGTGTCTGACC

TGCAGCGTCAGCGAAA

TAAATTCTGCTAGTGTCCGGTTTGC

CGGATACGCGCGAGAACTGACGACAACTCAGCGA

Sequence assembly

Contig 1 Contig 2

Finishing

What do you do think is the better option for everyday sequencing

use in the real world: Dideoxy or shotgun genome?

SQ10. Why not 1X? How much of the sequence would thereby be determined?

Drosophila genome(~100 million nt)

SAMPLE

. . .

How many 500 nt samples needed 100 million nt?100 000 000 500

I'm not really sure how to go about figuring out how much 1X of the

genome would be. How much what? Is this referring to nucleotides or contigs?

Paint the wall

How long will this take?


Paint the wall



Paint the wall


40 "

25 "

1 sq "


Paint the wall


40 "

25 "

1000paint balls?


Paint the wall


40 "

25 "

1 sq "


Do more clones generate a more accurate genome assembly?

0

0.1

0.2

0.3

0.4

0.5

0.6

0.7

0.8

0.9

1

0 2 4 6 8 10

Oversampling

Com

plet

enes

s How much is painted with 1x oversampling?


What are gapped palindromes? ...how we can design an

algorithm to do this in normal english


GATATCA palindrome?




GATCATCA palindrome?




GATCATCA palindrome?




A palindrome?

Problem Set 1

Paint the wall


40 "

25 "

1 sq "


2Firras

LawanginSonia

1Farah

KristenSandrine

Sue

3KavyaMandi

Supriya

5Franklin

SoniaTrevor

4Grace

JonathanKeith

Yordanos

7BobbyKathy

MoshrafTayab

6AbdallahCeleste

Tori

Me

FRONT

Problem Set 2, #3g: PalindromeSQ10: CoverageProblem Set 3, #1: Assembly

SQ14. From figures given in the text and in Table 1, check the accuracy of each of the following statements: a. "We produced 3.156 million reads that yielded 1.76 Gbp of sequence. . ." b. ". . .trillions of overlaps between reads are examined." c. ". . .to produce 654,000 of the 2-kbp mates and 497,000 of the 10-kbp mates."

Myers et al (2000)

how to read and understand the tables and the figures

they represent in reference to the sequencing.


Myers et al (2000)

Is it okay if we answer the questions of the tour using the internet instead of answering them just through the article?


Myers et al (2000)

I'm having trouble setting up the calculations in a

way to help me solve SQ14.

SQ13. Consider the data types listed in Table 1.

Why is each important?

Myers et al (2000)

TATA boxes before genes?


. . .

Focus on one nucleotide…What’s the probability that it’s covered by one read?What’s the probability that it’s covered by two reads?

What’s the probability that it’s covered by 200,000 reads?

Questometer Report

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Introduction to Bioinformatics Tuesday, 29 January