The Molecular Biology Notebook Online
A Beginners' Guide to Molecular Biology

---

Primer

---

Small fragment of single stranded DNA used in PCR reactions or sequencing. It hybridize to a complementary sequence on the template DNA.

View Dr Chromo's lecture on 'PCR'.

---

Pronounce:

---

Related Links

This is a search for primer in our database

• Design PCR Primers: tools: A list of free web applications to design PCR primers: including alignment primers, primers for RAPDS and from protein sequences. This team has done a great job at reviewing what is there.
• DNA from the beginning: A multimedia primer on the basis of DNA and heridity
• FastPCR Online Manual: FastPCR is free PCR primer and probe design software. It is efficient for standard, long, real-time PCRs, for inverse PCR, direct amino acid sequence degenerate PCR, multiplex PCR, LUX primers design for quantitative PCR, automatically SSR loci detection and direct PCR primers design, and in silico PCR. It can also perform sequence alignments, clustering and any kind repeat sequence searching.
• PCR Primer Design Guidelines: Good primer design is essential for successful reactions. The important design considerations described below are a key to specific amplification with high yield.
• Primer on Molecular Genetics: Primer on Molecular Genetics
• Primer on Molecular Genetics (Department of energy): This primer was prepared by Denise Casey (Human Genome Management Information System - Oak Ridge National Laboratory) for the 1991-92 DOE Human Genome Program Report and modified for Web access by Dan Jacobson.
• PrimerBlast: a primer design tool from NCBI: Finding primers specific to your PCR template (using Primer3 and BLAST).
• Protocol Online: This site contains useful protocols and reference material of all kinds mainly for the bench scientists, but by far the most useful part is the Bioforum Archive. This site can be very useful, particularly when you are doing a new procedure that no one in the lab has done. Just type in a query if you are having difficulty in the lab, eg qPCR primer design, and read where other people get stuck and solutions etc. The comments are well written (usually) and concise. Usually the questions get answered too which is a bonus.
• UGENE - Unipro: UGENE is a free cross-platform genome analysis suite. Multiple sequence alignment using MUSCLE 3,4 and KAlign; HMM profiles build and search, based on the source of HMMER 2 and HMMER 3; PCR Primers design using Primer 3; Protein secondary structure prediction using GOR IV and PSIPRED; Phylogenetic analysis with Phylip; Search for restriction enzymes and integration with REBASE; Extremely fast repeat finder; DNA reference assembly using Bowtie; Search for transcription factor binding sites using SITECON; Protein back translation; ORF finder; Complete Smith-Waterman algorithm implementation; Comparing genomes using dotplot view.

primer on Wikipedia

primer at Answers. com

---

Copyright Rothamsted Research 1999- 2010
Web technical : Nathalie Castells-Brooke

---