BTEC 3301

Websites for Protein Localization and Targeting

TMHMM, Phobius, and SignalP

Websites for Protein Visualization (3D structures)

JMOL, PDB, and AlphaFold

Website for Protein Sequence, Motifs, and Active Sites

InterPro, Uniprot, NCBI Graphics, CDD, and PROSITE

Websites for General Sequence Database

NCBI Protein and Uniprot

What does BLAST stand for?

Basic Local Alignment Search Tool

What does JMOL stand for?

Judgement as a Matter of Law

What does NCBI stand for?

National Center for Biotechnology Information

What does CDD stand for (in NCBI)?

Conserved Domains Database

A PDB identification number stands for?

Protein Data Bank

PAM stands for ...?

Point Accepted Mutation

BLOSUM stands for...?

BLOcks SUbstitution Matrix

The difference between PAMx and BLOSUMx is that?

1. PAM is based off evolutionary years whereas BLOSUM is based off identical with any member of the group

..

PAM30 is 30 million years ago into evolution whereas BLOSUM30 is 30% identical to the members of the group that is being compared.

In order to reduce noise you adjust the (1) and (2).

In order to reduce noise you adjust the WINDOW and THRESHOLD.

When you have many repeated motifs/regions in a dotmatcher you have ___________ complexity regions.

When you have many repeated motifs/regions in a dotmatcher you have LOW complexity regions.

What are the 3 types of sequence alignment?

1. Global

2. Semi-Global

3. Local

Global aligment

overall optimize alignment between two sequences

Semi-global alignment

NO PENALTY for gap ends

local alignment

match only some conserved sequences

What is Dynamic Programming?

more than one alignment may give the optimal score

A global alignment will have all ________ numbers on the first row and column.

A global alignment will have all NEGATIVE numbers on the first row and column.

A semi-global alignment will have the number _______ on the first row and column and ______.

A global alignment will have the number ZERO on the first row and column and then NEGATIVE numbers.

A local alignment will have _____ and ______.

A local alignment will have ZERO and NO negative numbers

EMBOSS Needle is used for ...

Global and you mark TRUE for end gap penalty option

EMBOSS Water is used for ...

Local

BLASTP is used for

Protein ----> Protein

BLASTN is used for

DNA -----> DNA

BLASTX is used for

DNA -----> Protein

TBLASTN is used for

Protein -----> DNA

TBLASTX is used for

DNA ----> DNA

For significance of hist BLAST cut off are a sequence identity of ___% or more for protein and ___% or more for nucleotide.

35%

70%

For significance of hist BLAST cut off are a hit of ________or less for protein and _________ or less for nucleotide.

E-values 10^-5 or less

E-values 10^-6 or less

What is an INDEL?

insertion or deletion mutation