PCR is a very diffused technique to amplify nucleic sequences by means of specific primers, that are continuously developed and published on international journals. Sometimes transcription mistakes can occur and erroneous primer sequences can be published, resulting in unexpected results if experiments are replicated. Although primers are relatively short, a rapid system for checking the correctness of the transcribed sequences could mitigate this problem. Verification codes are already used in other disciplines to guarantee the correctness of codified information. In this work an algorithm has been defined and the related software tool developed to fill this gap. A generic algorithm based on the ASCII coding of characters and their position within the sequence has been defined to generate a specific code on the basis of the sequence composition. Configuration parameters such as amount of characters and coding syntax have been left open for modification and personalisation. Microsoft Visual Studio 2005 has been used to compile “DelioCode” (Descriptive Literal Oligonucleotides Code), a Windows application featuring the algorithm and available on the web for download. The default algorithm has been used to verify the correctness of several sequences by testing casual primers with induced mistakes and primers published sequentially by different authors. All induced mistakes were detected by comparing the verification codes. On the basis of DelioCode, some typos have been found in primers sequences published in peer reviewed journals, and PCR repetition with these wrong primer sequences did not result in DNA amplification. The DelioCode programme is a tool for rapidly generating a unique code on the basis of a specific sequence. The shortness of the performed verification codes allows a rapid comparison among the sequences to find the common mistakes. This is useful every time researchers need to check the correctness of specific sequences, such as when sequences are transcribed from published articles or when oligonucleotidic primers are orderable by compilation of on-line forms. The diffusion of the verification codes generated by the programme would avoid typing mistakes in the transcription and would allow to save time in old-fashioned manual double-checking. The generation of specific codes for every primer could be evaluated to create a freeware “verified primer sequences bank”, where scientists could find rapidly specific primers already tested and published.

“DELIOCODE”: A FREEWARE PROGRAM FOR COMPARING OLIGONUCLEOTIDIC SEQUENCES BY VERIFICATION CODES.

PREZIUSO, Silvia;CUTERI, Vincenzo
2008-01-01

Abstract

PCR is a very diffused technique to amplify nucleic sequences by means of specific primers, that are continuously developed and published on international journals. Sometimes transcription mistakes can occur and erroneous primer sequences can be published, resulting in unexpected results if experiments are replicated. Although primers are relatively short, a rapid system for checking the correctness of the transcribed sequences could mitigate this problem. Verification codes are already used in other disciplines to guarantee the correctness of codified information. In this work an algorithm has been defined and the related software tool developed to fill this gap. A generic algorithm based on the ASCII coding of characters and their position within the sequence has been defined to generate a specific code on the basis of the sequence composition. Configuration parameters such as amount of characters and coding syntax have been left open for modification and personalisation. Microsoft Visual Studio 2005 has been used to compile “DelioCode” (Descriptive Literal Oligonucleotides Code), a Windows application featuring the algorithm and available on the web for download. The default algorithm has been used to verify the correctness of several sequences by testing casual primers with induced mistakes and primers published sequentially by different authors. All induced mistakes were detected by comparing the verification codes. On the basis of DelioCode, some typos have been found in primers sequences published in peer reviewed journals, and PCR repetition with these wrong primer sequences did not result in DNA amplification. The DelioCode programme is a tool for rapidly generating a unique code on the basis of a specific sequence. The shortness of the performed verification codes allows a rapid comparison among the sequences to find the common mistakes. This is useful every time researchers need to check the correctness of specific sequences, such as when sequences are transcribed from published articles or when oligonucleotidic primers are orderable by compilation of on-line forms. The diffusion of the verification codes generated by the programme would avoid typing mistakes in the transcription and would allow to save time in old-fashioned manual double-checking. The generation of specific codes for every primer could be evaluated to create a freeware “verified primer sequences bank”, where scientists could find rapidly specific primers already tested and published.
2008
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Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/11581/111248
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