TY - JOUR
T1 - FastPCR
T2 - An in silico tool for fast primer and probe design and advanced sequence analysis
AU - Kalendar, Ruslan
AU - Samuilova, Olga
AU - Ivanov, Konstantin I.
N1 - Funding Information:
Java Web tools are publicly available and may not be reproduced or distributed for commercial use. This work was supported by Primer Digital Ltd. and was partially supported by the Science Committee of the Ministry of Education and Science of the Republic of Kazakhstan (grant 5135/GF4).
Publisher Copyright:
© 2017 Elsevier Inc.
Copyright:
Copyright 2020 Elsevier B.V., All rights reserved.
PY - 2017/7
Y1 - 2017/7
N2 - Polymerase chain reaction (PCR) is one of the most important laboratory techniques used in molecular biology, genetics and molecular diagnostics. The success of a PCR-based method largely depends on the correct nucleic acid sequence analysis in silico prior to a wet-bench experiment. Here, we report the development of an online Java-based software for virtual PCR on linear or circular DNA templates and multiple primer or probe search from large or small databases. Primer or probe sensitivity and specificity are predicted by searching a database to find sequences with an optimal number of mismatches, similarity and stability. The software determines primer location, orientation, efficiency of binding and calculates primer melting temperatures for standard and degenerate oligonucleotides. The software is suitable for batch file processing, which is essential for automation when working with large amounts of data. The online Java software is available for download at http://primerdigital.com/tools/pcr.html. Accession numbers for the sequences resulting from this study: EU140956 EU177767 EU867815 EU882730 FJ975775-FJ975780 HM481419 HM481420 KC686837–KC686839 KM262797
AB - Polymerase chain reaction (PCR) is one of the most important laboratory techniques used in molecular biology, genetics and molecular diagnostics. The success of a PCR-based method largely depends on the correct nucleic acid sequence analysis in silico prior to a wet-bench experiment. Here, we report the development of an online Java-based software for virtual PCR on linear or circular DNA templates and multiple primer or probe search from large or small databases. Primer or probe sensitivity and specificity are predicted by searching a database to find sequences with an optimal number of mismatches, similarity and stability. The software determines primer location, orientation, efficiency of binding and calculates primer melting temperatures for standard and degenerate oligonucleotides. The software is suitable for batch file processing, which is essential for automation when working with large amounts of data. The online Java software is available for download at http://primerdigital.com/tools/pcr.html. Accession numbers for the sequences resulting from this study: EU140956 EU177767 EU867815 EU882730 FJ975775-FJ975780 HM481419 HM481420 KC686837–KC686839 KM262797
KW - Degenerate PCR
KW - DNA fingerprinting
KW - DNA primers
KW - Genetic engineering tools
KW - Isothermal amplification of nucleic acids
KW - Nucleic acid hybridization
KW - PCR primer and probe analysis
KW - Polymerase chain reaction
KW - Primer binding site
KW - Probe
UR - http://www.scopus.com/inward/record.url?scp=85019592209&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85019592209&partnerID=8YFLogxK
U2 - 10.1016/j.ygeno.2017.05.005
DO - 10.1016/j.ygeno.2017.05.005
M3 - Article
C2 - 28502701
AN - SCOPUS:85019592209
SN - 0888-7543
VL - 109
SP - 312
EP - 319
JO - Genomics
JF - Genomics
IS - 3-4
ER -
