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.

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Dynamic Programming

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Dynamic programming

Dynamic Programming

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


Question is

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

You are in the driver’s seat

  • What is the most important?

    • Exact nucleotide match?

    • One-for-one (no gaps)?

    • Length


Mathematical model

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

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

Assign a value to each situation

  • Identical: +5

  • Mismatch: -2

  • Insertion or deletion: -6

    (Could have others; could choose different values)


Dynamic programming

http://www.acm.org/crossroads/xrds13-1/dna.html


Dynamic programming

  • 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


Dynamic programming

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

AAD3539

Animalia

Bacteria

0.1


Dynamic programming

  • 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?


Dynamic programming

Arabidopsis AMY1

Clade I

Secreted

421-445 aa

rice 2A

barley A

barley B

morning glory

rice 3B

dodder

maize

adzuki bean

rice 3E

rice XP_472377

Arabidopsis AMY2

apple 10

cassava

apple 9

kiwifruit

apple 8

potato

plantain

Clade II

Cytosolic

407-414 aa

Clade III

Plastidic

877-906 aa

Arabidopsis AMY3

rice NP_916641


Dynamic programming

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


Dynamic programming

  • Use alignments to look for:

    • Structures important for common

      • functions (orthologs)

    • Structures important for unique

      • functions (paralogs)

    • Unusual structures


Dynamic programming

N

C

AMY1 has a three amino acid deletion

AtAMY1

3


Dynamic programming

Barley -amylase

Red: NHDTGST

Blue: VAEIW

Active site residues


Dynamic programming

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

AtAMY1


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