Bioinformatics Week 3 Day 3 Notes

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Clustal W :

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is a program used for multiple sequence alignment.
Uses GLOBAL SEQUENCE ALIGNMENT

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Uniprot kB :

Back 2

Universal protein knowledge base
Is a large protein databases that contains all protein sequences and ot gets updated frequently.

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Expasy:

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Expert Protein Analysis System is a large Protein server –
Contains many protein databases such as UniProt kB

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Phylogenetics:

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Phylogenetics: (STUDY OF PHYLOGENY)

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1. Phylogeny =
2. Phylogeny Tree ;

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1. is analysis of relationships between genes or organisms based on evolutionary time or common ancestor.
2. is a diagram that shows the results of phylogeny

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1 ) Phylogram –

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is a type of phylogenetic tree that shows the relationshops between genes or organisms , based on evolutionary time.

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2) Cladogram ;

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is a type of phylogenetic tree that shows therelationship between genes or organisms based on a common ancestor , NOT ON EVOLUTIONARY TIME.

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We search for proteins by their ..What?

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MASS

Front 9

Protein mass is in ?

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Protein mass is in “Dalton” (Da) or KiloDalton (Kda)

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Tm =

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Annealing or melting temp. 55-65C-

Front 11

calculate the optimal Tm

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Tm=4(c+G) +2(A+T)0C

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Expasy stands for -

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Expert Protein Analysis System