Primer Desighning Tools (practicle)

DNA Template and oligonucleotide primers must be considered in greater detail (Linz et al., 1990).
Efficacy and sensitivity of PCR largely depend on the efficiency of primers (He et al., 1994).

There are many tools for primer designing and doing different tasks related to primer:

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 Primer Desighning Tools (practicle)

There will be described two tools of them

1. Primo Degenerate 3.4

2. Primer Design (PRIDE 2.0)

Primo Degenerate 3.4:

Primo Degenerate 3.4 designs PCR primers based on a single peptide sequence or multiple alignments of
proteins or nucleotides.

http://www.changbioscience.com/primo/primod.html

1. first take protein name and search for neucleotide sequence of it.on its home page
 http://www.ncbi.nlm.nih.gov/guide/
2. then select a mRna sequence
 http://www.ncbi.nlm.nih.gov/nuccore/AY890601.1

ACCESSION: AY890601

Synthetic construct Homo sapiens clone FLH134844.01X chemokine (C-C motif) ligand 20 (CCL20) mRNA,
complete cds

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 Primer Desighning Tools (practicle)
ATGTGCTGTACCAAGAGTTTGCTCCTGGCTGCTTTGATGTCAGTGCTGCTACTCCACCTCTGCGGCGAAT
CAGAAGCAAGCAACTTTGACTGCTGTCTTGGATACACAGACCGTATTCTTCATCCTAAATTTATTGTGGG
CTTCACACGGCAGCTGGCCAATGAAGGCTGTGACATCAATGCTATCATCTTTCACACAAAGAAAAAGTTG
TCTGTGTGCGCAAATCCAAAACAGACTTGGGTGAAATATATTGTGCGTCTCCTCAGTAAAAAAGGCAAGA
ACATGTAG
3. then open the link paste sequence in input spacethen press go button belowthere on the screen

4. Result will be shown there in next blank space to the input space.

Primer Design (PRIDE 2.0):

PRIDE is a primer design program that automatically designs primers in single contigs or whole
sequencing projects to extend the already known sequence and to double strand single-stranded
regions.

http://ibios.dkfz.de/tbi_old/services/Pride/search_primer

1. Put sequence in input bar and then press submit.

2. Result will be shown in next window with link

http://ibios.dkfz.de/tbi_old/services/Pride/nph-search_primer

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 Primer Desighning Tools (practicle)

 Result

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