Bioinformatics Quiz 3 Review Pairwise Alignment,criteria For Primer Design

Front 1

to avoid Primer dimertization -

Back 1

calculate the optimal Tm, (temperature), and use it in the PCR.

Front 2

WHITISH BAND AT THE BOTTOM OF THE GEL INDICATES WHAT?

Back 2

PRIMER DiMERS

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WHAT IS A PRIMER DIMER OR PRIMER DIMERIZATION?

Back 3

primer dimers are primers that bind to each other instead of the intended DNA to be amplified.

Front 4

Define;

1. BLASTn -
2. BLASTp -
3. BLASTx -

Back 4

1. BLASTn - BLASTn is used for comparing nucleotide sequences.
2. BLASTp - used to search for protein sequences.
3. BLASTx - used to compare known nucleotide to matching transslated protein sequences in the database

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what program is used fir primer design?

Back 5

NCBI/ Primer-BLAST: Finding primers specific to your PCR template (using Primer3 and BLAST).
and / OR / frodo.wi.mit.edu/

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What is the criteria for primer design?

Back 6

1. Length 18 - 24 (nt) nucleotiudes
2. Tm = Annealing / melting temperature 48C - 72C
3. G/C% between 40% - 80%
4. no hairpin loops.

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denaturing occurs in what temperature range?

Back 7

90* to 95*C

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Annealing occurs at What temperaturees?

Back 8

48*C - 72*C Annealing ocurrs

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Extension occurs in what temperature range?

Back 9

Extension occurs between 68*C -72*C.

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target DNA is ?

Back 10

Target DNA is the segment of DNA to be amplified

Front 11

nucleotides alwways attach at ?

Back 11

3' H

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primers are?

Back 12

short single stranded dna
they initiatte dna amplification.

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What is Taq polymerase ?

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Taq polymerase is a thermostable DNA polymerase named after the thermophilic bacterium Thermus aquaticus from which it was originally isolated by Thomas D. Brock in 1965 Taq's optimum temperature for activity is 75–80°C, with a half-life of greater than 2 hours at 92.5°C, 40 minutes at 95°C and 9 minutes at 97.5°C, and can replicate a 1000 base pair strand of DNA in less than 10 seconds at 72°C.[4]

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left primers are also called, ?

right primers are also called, ?

Back 14

forward primer or sence primers

reverse primers or antisence primers

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ivbio.bio.indiana.edu IS A SITE FOR WHAT?

Back 15

phylodendron web program used to cxreate phylogtrams and phylogenic trees andwhich organisms have similar sequences of dsna of interest

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CLUSTAL W IS WHAT?

Back 16

Clustal is a widely used multiple sequence alignment computer program. ClustalW produces biologically meaningful multiple sequence alignments of divergent sequences. It calculates the best match for selected sequences and lines them up, so identities, similarities, and differences can be identified. ClustalW can be useful:

1. When designing experiments to test and modify the function of specific proteins
2. In predicting the function and structure of proteins
3. In identifying new members of protein families

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Definition for blastn:

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nucleotide–nucleotide BLAST. blastn takes nucleotide sequences in FASTA format, GenBank Accession numbers, or GI numbers and compares them against the NCBI Nucleotide databases.

www.ncbi.nlm.nih.gov/books/NBK21106/

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Definition for BLASTx :

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A BLAST program that compares the six-frame conceptual translation products of a nucleotide query sequence (both strands) against a protein sequence database. The user must enter a NUCLEOTIDE sequence and select a PROTEIN database for the search.
dictybase.org/db/html/help/glossary.html

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Definition for BLASTp :

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protein–protein BLAST. blastp takes protein sequences in FASTA format, GenBank Accession numbers, or GI numbers and compares them against the NCBI Protein databases.
www.ncbi.nlm.nih.gov/books/NBK21106/

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PCR involves the following three steps:

Back 20

Denaturation, Annealing and Extension.

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Tm is , ?

Back 21

Melting temp. of a product in pcr

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PCR – NEEDS TO HAVE ...?

Back 22

PCR – NEEDS TO HAVE THE SEQUENCE OF DNA TO BE AMPLIFIED

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What is a pairwise alignment?

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Pairwise sequence alignment methods are used to find the best-matching piecewise (local) or global alignments of two query sequences. Pairwise alignments can only be used between two sequences at a time, but they are efficient to calculate and are often used for methods that do not require extreme precision (such as searching a database for sequences with high similarity to a query).

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The three primary methods of producing pairwise alignments are

Back 24

dot-matrix methods, dynamic programming, and word methods;[1] however, multiple sequence alignment techniques can also align pairs of sequences.

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1. A primer that amplifies the Sence strand is called ?

2. A primer that amplifies the antisence strand is called?

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1. A Left, Forward or Sence Primer.

2. A Right , Reverse or Antisence Primer

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transcript variant ?

Back 26

Variations in the genes transcriptions due to an alternative splicing in pre-mRNA.

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1. EMBL =
2. DDBJ =
3. OMIM =

Back 27

1. DATA BASE FOR ALL KNOWN RNA + DNA PROTEINS IN EUROPE.
2. DATABASE FOR ALL KNOWN PROTEINS DNA AND RNA IN JAPAN.
3. ONLINE MENDELIAN INHERITANCE IN MAN. CONTAINS ALL KNOWN GENETIC DISEASES.

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CDS =

Back 28

CODED SEQUENE AREA