Dynamic Programming
-
Upload
lilah-horton -
Category
Documents
-
view
14 -
download
0
description
Transcript of Dynamic Programming
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
0.1
Tp GAA
Bh BAB0442
Bt Aglu-III
Ss xylS
Lp XylQTm
AAD3539
Aa GlcA
Sc CAB8890
Ce AAA8317
Lv GAA
Hs S/I-C
Hs S/I-N
Cj GAAI
Cj GAAII
Hs GAA
Hv Aglu
At Aglu-1
Bv Aglu
So Aglu
Pp BAB3946
St MAL2
AtXYL1
TmXYL
MjAglu Pt Aglu
Sp Aglu
Anig aglA
An AgdA
Ca GAM1
Soc GAM1
An agdB
Fungi
Protista
Bacteria
Plantae
Animalia
Archaea
Plant -amylases are located in different cellular compartments
Plastids (chloroplasts, amyloplasts)CytosolApoplast (cell wall space)
What is the function of the non-plastid forms?
dodder
adzuki bean
morning glory
rice 2Abarley A
barley B
rice 3B
maize
rice 3E
rice XP_472377
cassava
apple 9
apple 8
potato plantain
rice NP_916641
kiwifruit
apple 10
Clade ISecreted
421-445 aa
Clade IICytosolic
407-414 aa
Clade IIIPlastidic
877-906 aa
Arabidopsis AMY1
Arabidopsis AMY2
Arabidopsis AMY3
Homologous sequences (homologues)Share a common ancestor
ParalogsHomologues derived by gene duplicationFunctions may varyLook for differences
OrthologsHomologues derived by speciationCommon functionLook for similarities
Use alignments to look for:
• Structures important for common functions (orthologs)
• Structures important for unique functions (paralogs)
• Unusual structures