FastPCR protocols

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FastPCR specifications

Information


Unique identifier OMICS_02336
Name FastPCR
Software type Application/Script, Package/Module
Interface Command line interface
Restrictions to use License purchase required
Operating system Unix/Linux, Windows
Programming languages Java
Computer skills Medium
Version 6.6.02
Stability Stable
Free trial Yes
Maintained Yes

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Documentation


Maintainers


  • person_outline FastPCR Team <>
  • person_outline Ruslan Kalendar <>
  • person_outline Bekbolat Khassenov <>
  • person_outline Erlan Ramanculovb <>
  • person_outline Olga Samuilova <>
  • person_outline Konstantin Ivanov <>

Information


Unique identifier OMICS_02336
Name FastPCR
Software type Application/Script
Restrictions to use None
Programming languages Java
Computer skills Medium
Stability Stable
Maintained Yes

Documentation


Maintainers


  • person_outline FastPCR Team <>
  • person_outline Ruslan Kalendar <>
  • person_outline Bekbolat Khassenov <>
  • person_outline Erlan Ramanculovb <>
  • person_outline Olga Samuilova <>
  • person_outline Konstantin Ivanov <>

Publications for FastPCR

FastPCR in pipelines

 (5)
2016
PMCID: 4718150
PMID: 26819544
DOI: 10.4137/EBO.S35158

[…] genome sequence, which was downloaded from the ncbi website (http://www.ncbi.nlm.nih.gov/)., as shown in the workflow in , as a first step to identify a novel ltr in the genome of oryza rice we used fastpcr professional 6.5 or the ltr_finder program (http://tlife.fudan.edu.cn/ltr_finder/) to search the nipponbare genome with default parameters. the output ltrs were then manually inspected […]

2016
PMCID: 4845337
PMID: 27112435
DOI: 10.1186/s13104-016-2039-x

[…] (>50 bp) on each side of the repeated units as ‘‘potentially amplifiable loci’’ i.e. pal [, ]. for subsequent analyses, we randomly selected 19 loci among all pal. primer pairs were designed with fastpcr v. 6.0 [] to avoid primer dimers, self-annealing and hairpin formation when multiplexing loci during pcr. in addition, primers were designed to have very similar melting temperatures to avoid […]

2015
PMCID: 4524895
PMID: 26300899
DOI: 10.3389/fpls.2015.00602

[…] kit (clontech, laboratories, mountain view, ca), according to the manufacturer's instructions. the protein encoded by the open reading frame (orf) of the ah24 cdna was deduced with the aid of the fastpcr 6.0 program (http://en.bio-soft.net/pcr/fastpcr.html). bioinformatic analyses were performed to determine the possible biological function of the ah24 protein and to search for conserved […]

2013
PMCID: 4105025
PMID: 25202552
DOI: 10.3732/apps.1200450

[…] of all or most of the species. we selected loci (generally only a small portion of a gene) that comprised a single, long exon (200 bp) with matches in multiple species, and designed primers with fastpcr (primerdigital ltd., helsinki, finland; http://www.primerdigital.com/fastpcr.html) for their amplification using default settings. the presence of introns was tested by comparison […]

2012
PMCID: 3504151
PMID: 23185413
DOI: 10.1371/journal.pone.0049705

[…] may 2012) to assist in locating potential gene fusions. three spanning reads and two split reads were required to call sequence reads a gene fusion., primers used in pcr were designed with the fastpcr software . the full list of applied primers is given in . the primers used for detection of the hey1- ncoa2 fusion were identical to the primers used by wang et al . cdna pcr was run using 2 […]


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FastPCR in publications

 (85)
PMCID: 5930771
PMID: 29720087
DOI: 10.1186/s12864-018-4700-3

[…] those obtained from microarray to validate the data. target cdna sequences were derived from contig probe sequences within affymetrix barley1 genechip genome array. pcr primers were designed using fastpcr software (primer design ltd., finland), and their specificity was verified by a blast search of the netaffx™ analysis center and ncbi databases., real time transcription values was calculated […]

PMCID: 5802496
PMID: 29317596
DOI: 10.1038/s41398-017-0061-y

[…] by a standard protocol. for covering coding regions of grin1, grin2a, grin2c, grin2d, grin3a, and grin3b (human reference sequence ncbi (build 37)), we designed custom amplification primers by fastpcr (primerdigital ltd, helsinki, finland) and ncbi primer-blast. the ion library equalizer kit adapters and ion ampliseq library kits 2.0 (thermo fisher scientific, foster city, ca, usa) […]

PMCID: 5738103
PMID: 29258559
DOI: 10.1186/s13071-017-2575-9

[…] 58 °c to 62 °c, primer length of 20 to 21 bp, primer g/c content of approximately 50%, and amplicon length of 100–200 bp. potential self-complementarity and primer-dimer formation were checked using fastpcr professional software (http://primerdigital.com/fastpcr.html). the efficiency of primers used in rt-qpcr was calculated in the biomark real-time pcr system, and only primers […]

PMCID: 5856900
PMID: 29234880
DOI: 10.1007/s00425-017-2827-0

[…] selected for the analysis (table ). the remap method used primer combinations of microsatellite sequences and retrotransposons sequences (table ). of the 50 combinations tested, 16 were selected. fastpcr was used to design primers for retrotransposon sequences (kalendar et al. ). angela retrotransposon primers were designed using sequences from the ncbi database with ay485644 accession […]

PMCID: 5688051
PMID: 29143146
DOI: 10.1186/s40529-017-0200-z

[…] containing microsatellites were detected using tandem repeats finder version 4.09 (benson ), and primer pairs were designed for microsatellite loci with suitable flanking regions to amplify using fastpcr software version 6.5.94 (kalendar et al. ). each primer pairs were designed to amplify with a fragment in the range of 100–400 bp., to verify the effectiveness and polymorphisms of 28 […]


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FastPCR institution(s)
PrimerDigital Ltd, Helsinki, Finland; RSE "National Center for Biotechnology" under the Science Committee, Ministry of Education and Science of the Republic of Kazakhstan, Astana, Kazakhstan; Department of Biochemistry, I.M. Sechenov First Moscow State Medical University, Moscow, Russia; Department of Biophysics, Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, Russia
FastPCR funding source(s)
Supported by Primer Digital Ltd. and by the Science Committee of the Ministry of Education and Science of the Republic of Kazakhstan (grant 5135/GF4).

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