dynamic programming
Download
Skip this Video
Download Presentation
Dynamic Programming

Loading in 2 Seconds...

play fullscreen
1 / 23

Dynamic Programming - PowerPoint PPT Presentation


  • 55 Views
  • Uploaded on

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.

loader
I am the owner, or an agent authorized to act on behalf of the owner, of the copyrighted work described.
capcha
Download Presentation

PowerPoint Slideshow about ' Dynamic Programming' - lilah-horton


An Image/Link below is provided (as is) to download presentation

Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author.While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server.


- - - - - - - - - - - - - - - - - - - - - - - - - - E N D - - - - - - - - - - - - - - - - - - - - - - - - - -
Presentation Transcript
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)

slide13

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
slide15

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

slide17

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?
slide18

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

slide19

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

slide20

Use alignments to look for:

    • Structures important for common
      • functions (orthologs)
    • Structures important for unique
      • functions (paralogs)
    • Unusual structures
slide21

N

C

AMY1 has a three amino acid deletion

AtAMY1

3

slide22

Barley -amylase

Red: NHDTGST

Blue: VAEIW

Active site residues

ad