# Dynamic Programming - PowerPoint PPT Presentation

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Dynamic Programming. How to match up sequences and have the matches make sense and be quantitative. Question is. How does a specific sequence compare to one other specific sequence? Is it similar? If so, at what level? Can’t compare every base to every other base--to complex.

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Dynamic Programming

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## Dynamic Programming

How to match up sequences and have the matches make sense and be quantitative

### Question is

• How does a specific sequence compare to one other specific sequence?

• Is it similar?

• If so, at what level?

• Can’t compare every base to every other base--to complex

### You are in the driver’s seat

• What is the most important?

• Exact nucleotide match?

• One-for-one (no gaps)?

• Length

### Mathematical model

• Derive equation for each position, based on your value system

• Methodically go through each base for each sequence and calculate the value

• At the end, find the optimal path

### Starting point: three possible scenarios for each position in sequences X and Y

• At a given position, the bases (Xm and Yn) are identical in X and Y

• At a given position, the base (Xm) in X is aligned with a gap in Y (and Yn appeared earlier)

• At a given position, the base in Y is aligned with a gap in X (and Xm appeared earlier)

### Assign a value to each situation

• Identical: +5

• Mismatch: -2

• Insertion or deletion: -6

(Could have others; could choose different values)

• Alpha-glucosidase in plants:

• Enzymes sharing WIDMNE signature

• sequence

• alpha-glucosidase (all groups)

• alpha-xylosidase (plant, bacteria, archaea)

• Sucrase/Isomaltase (animal)

• Related sequences with broad substrate

• specificity

Mj

Aglu

Plantae

Fungi

At

XYL1

Pt Aglu

Tm

XYL

Sp Aglu

St MAL2

Anig aglA

Pp BAB3946

An AgdA

So Aglu

Ca GAM1

Bv Aglu

Soc GAM1

At Aglu-1

An agdB

Hv Aglu

Protista

Tp GAA

Hs GAA

Cj GAAII

Cj GAAI

Archaea

Ss xylS

Hs S/I-N

Hs S/I-C

Bt Aglu-III

Lv GAA

Ce AAA8317

Bh BAB0442

Aa GlcA

Lp XylQ

Sc

CAB8890

Tm

Animalia

Bacteria

0.1

• Plant -amylases are located in different cellular compartments

• Plastids (chloroplasts, amyloplasts)

• Cytosol

• Apoplast (cell wall space)

• What is the function of the non-plastid forms?

Arabidopsis AMY1

Secreted

421-445 aa

rice 2A

barley A

barley B

morning glory

rice 3B

dodder

maize

rice 3E

rice XP_472377

Arabidopsis AMY2

apple 10

cassava

apple 9

kiwifruit

apple 8

potato

plantain

Cytosolic

407-414 aa

Plastidic

877-906 aa

Arabidopsis AMY3

rice NP_916641

Homologous sequences (homologues)

Share a common ancestor

Paralogs

Homologues derived by gene duplication

Functions may vary

Look for differences

Orthologs

Homologues derived by speciation

Common function

Look for similarities

• Use alignments to look for:

• Structures important for common

• functions (orthologs)

• Structures important for unique

• functions (paralogs)

• Unusual structures

N

C

AMY1 has a three amino acid deletion

AtAMY1

3

Barley -amylase

Red: NHDTGST

Blue: VAEIW

Active site residues

Variation in the active site loop among plant and bacterial -amylases

AtAMY1