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# Dynamic Programming - PowerPoint PPT Presentation

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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## PowerPoint Slideshow about ' Dynamic Programming' - lilah-horton

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### Dynamic Programming

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

• 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

• What is the most important?

• Exact nucleotide match?

• One-for-one (no gaps)?

• Length

• 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 in sequences X and Y

• Identical: +5

• Mismatch: -2

• Insertion or deletion: -6

(Could have others; could choose different values)

• Alpha-glucosidase in plants: in sequences X and Y

• Enzymes sharing WIDMNE signature

• sequence

• alpha-glucosidase (all groups)

• alpha-xylosidase (plant, bacteria, archaea)

• Sucrase/Isomaltase (animal)

• Related sequences with broad substrate

• specificity

Mj in sequences X and Y

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 in sequences X and Y-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 in sequences X and YAMY1

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 in sequences X and Y (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: in sequences X and Y

• Structures important for common

• functions (orthologs)

• Structures important for unique

• functions (paralogs)

• Unusual structures

N in sequences X and Y

C

AMY1 has a three amino acid deletion

AtAMY1

3

Barley in sequences X and Y-amylase

Red: NHDTGST

Blue: VAEIW

Active site residues

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

AtAMY1