- 55 Views
- Uploaded on

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

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 in sequences X and Y

- Identical: +5
- Mismatch: -2
- Insertion or deletion: -6
(Could have others; could choose different values)

http://www.acm.org/crossroads/xrds13-1/dna.html in sequences X and Y

- 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

AAD3539

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

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

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

- Structures important for common

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

AtAMY1

Download Presentation

Connecting to Server..