Bioinformatic Comparisons of Some Web-based PCR Primer Design Programs

Öz

Bioinformatics has become an indispensable tool for both basic and applied research in biotechnology in the life sciences. The polymerase chain reaction (PCR) is a laboratory method that can be used to quickly amplify a large number of identical copies of a specific DNA segment. In PCR, short synthetic DNA fragments known as primers are used to selectively amplify a specific section of the genome. For PCR to be as efficient and specific as possible, it is important to choose an effective primer sequence and use the correct concentration of primers. If the primer is not designed carefully, non-specific amplification and/or primer dimer formation may occur, which may prevent product formation. Currently, a number of different design tools are available on the internet to assist molecular geneticists in designing PCR primers under optimal conditions. In this study, out of 39 web-based PCR primer design programs, 7 accessible, freely available and widely used web-based PCR primer design programs (NCBI, Primer3, Biserach, Genscript and Primer3plus; Stitcher 2.0; and PrimerQest Tool) were compared using bioinformatics applications for genomic sequences. The advantages and disadvantages of the web-based PCR programs are discussed on the basis of the comparison results.

Anahtar Kelimeler

• Bioinformatics analysis
• Primer design
• Web-based PCR primers design programs

Web Tabanlı Bazı PCR Primer Tasarım Programlarının Biyoinformatik Karşılaştırılması

Öz

Biyoinformatik, yaşam bilimleri biyoteknolojisinde hem temel hem de uygulamalı araştırmalar için önemli bir araç haline gelmiştir. Polimeraz zincir reaksiyonu (PCR), DNA'nın belirli bir bölümünün çok sayıda özdeş kopyasını hızla çoğaltmak için kullanılan bir laboratuvar yöntemidir. PCR, genomun belirli bir bölümünü seçici olarak çoğaltmak için primer adı verilen kısa sentetik DNA parçalarını kullanır. PCR'nin mümkün olduğu kadar verimli ve spesifik olması için etkili bir primer dizisinin seçilmesi ve doğru primer konsantrasyonunun kullanılması önemlidir. Primer dikkatli bir şekilde tasarlanmadığı sürece spesifik olmayan amplifikasyon ve/veya primer dimer oluşumu meydana gelebilir ve bu durum hedeflenen PCR ürününün oluşumunu engelleyebilir. Günümüzde moleküler genetikçiler için optimum koşullarda PCR primerleri oluşturmasına yardımcı olacak çeşitli tasarım araçlarına internette kolaylıkla erişilebilir. Bu çalışmada erişilebilir, kullanıma açık ve yagın olarak kullanılan 39 adet web tabanlı PCR primer tasarım programlarından, 7 adet web tabanlı PCR primer tasarım programları (NCBI, Primer3, Biserach, Genscript, Primer3plus, Stitcher 2.0, PrimerQest Tool) biyoinformatik tabanlı genomik dizi uygulamaları ile karşılaştırılmıştır. Karşılaştırma sonuçlarına göre web tabanlı PCR programlarının kullanım üstünlükleri ile olumsuz yanları tartışılmıştır.

Anahtar Kelimeler

• Biyoinformatik analiz
• Primer tasarımı
• Web tabanlı PCR primer tasarım programları

Kaynakça

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