FastPCR Software for PCR, In Silico PCR, and Oligonucleotide Assembly and Analysis View Full Text


Ontology type: schema:Chapter      Open Access: True


Chapter Info

DATE

2014

AUTHORS

Ruslan Kalendar , David Lee , Alan H. Schulman

ABSTRACT

This chapter introduces the software FastPCR as an integrated tools environment for PCR primer and probe design. It also predicts oligonucleotide properties based on experimental studies of PCR efficiency. The software provides comprehensive facilities for designing primers for most PCR applications and their combinations, including standard, multiplex, long-distance, inverse, real-time, group-specific, unique, and overlap extension PCR for multi-fragment assembly in cloning, as well as bisulphite modification assays. It includes a program to design oligonucleotide sets for long sequence assembly by the ligase chain reaction. The in silico PCR primer or probe search includes comprehensive analyses of individual primers and primer pairs. It calculates the melting temperature for standard and degenerate oligonucleotides including LNA and other modifications, provides analyses for a set of primers with prediction of oligonucleotide properties, dimer and G/C-quadruplex detection, and linguistic complexity, and provides a dilution and resuspension calculator. The program includes various bioinformatics tools for analysis of sequences with CG or AT skew, of CG content and purine-pyrimidine skew, and of linguistic sequence complexity. It also permits generation of random DNA sequence and analysis of restriction enzymes of all types. It finds or creates restriction enzyme recognition sites for coding sequences and supports the clustering of sequences. It generates consensus sequences and analyzes sequence conservation. It performs efficient and complete detection of various repeat types and displays them. FastPCR allows for sequence file batch processing, which is essential for automation. The FastPCR software is available for download at http://primerdigital.com/fastpcr.html and online version at http://primerdigital.com/tools/pcr.html . More... »

PAGES

271-302

Identifiers

URI

http://scigraph.springernature.com/pub.10.1007/978-1-62703-764-8_18

DOI

http://dx.doi.org/10.1007/978-1-62703-764-8_18

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1043493906

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/24395370


Indexing Status Check whether this publication has been indexed by Scopus and Web Of Science using the SN Indexing Status Tool
Incoming Citations Browse incoming citations for this publication using opencitations.net

JSON-LD is the canonical representation for SciGraph data.

TIP: You can open this SciGraph record using an external JSON-LD service: JSON-LD Playground Google SDTT

[
  {
    "@context": "https://springernature.github.io/scigraph/jsonld/sgcontext.json", 
    "about": [
      {
        "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/0802", 
        "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
        "name": "Computation Theory and Mathematics", 
        "type": "DefinedTerm"
      }, 
      {
        "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/08", 
        "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
        "name": "Information and Computing Sciences", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Computer Simulation", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "DNA Primers", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Inverted Repeat Sequences", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Microsatellite Repeats", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Nucleic Acid Denaturation", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Oligonucleotides", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Polymerase Chain Reaction", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Sequence Analysis, DNA", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Software", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Time Factors", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Transition Temperature", 
        "type": "DefinedTerm"
      }
    ], 
    "author": [
      {
        "affiliation": {
          "alternateName": "University of Helsinki", 
          "id": "https://www.grid.ac/institutes/grid.7737.4", 
          "name": [
            "MTT/BI Plant Genomics Laboratory, Institute of Biotechnology, University of Helsinki, Helsinki, Finland"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Kalendar", 
        "givenName": "Ruslan", 
        "id": "sg:person.01061032627.62", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01061032627.62"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "National Institute of Agricultural Botany", 
          "id": "https://www.grid.ac/institutes/grid.17595.3f", 
          "name": [
            "John Bingham Laboratory, National Institute of Agricultural Botany, Cambridge, UK"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Lee", 
        "givenName": "David", 
        "id": "sg:person.01303225202.04", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01303225202.04"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "University of Helsinki", 
          "id": "https://www.grid.ac/institutes/grid.7737.4", 
          "name": [
            "MTT/BI Plant Genomics Laboratory, Institute of Biotechnology, University of Helsinki, Helsinki, Finland"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Schulman", 
        "givenName": "Alan H.", 
        "id": "sg:person.0777404667.23", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0777404667.23"
        ], 
        "type": "Person"
      }
    ], 
    "citation": [
      {
        "id": "https://doi.org/10.1093/nar/28.9.1879", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1003733221"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/bioinformatics/bti134", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1006446393"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/nar/gkn198", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1006730464"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/nar/gkp026", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1006892534"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1073/pnas.95.4.1460", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1009187647"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1073/pnas.48.8.1390", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1011693507"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/bioinformatics/btg350", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1012323448"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1073/pnas.91.20.9549", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1014181108"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/nar/gks596", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1014785724"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/bioinformatics/17.12.1226", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1014919468"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nprot.2006.377", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1015945679", 
          "https://doi.org/10.1038/nprot.2006.377"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nprot.2006.377", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1015945679", 
          "https://doi.org/10.1038/nprot.2006.377"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/nar/gkq639", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1016305635"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.ygeno.2011.04.009", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1018579651"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/nar/30.3.e11", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1018841621"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/nar/24.18.3538", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1019513958"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1073/pnas.86.17.6686", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1019941969"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/nar/18.22.6531", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1022940325"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/s0006-3495(97)78756-3", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1027176605"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/nar/gkn191", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1027671874"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/0076-6879(92)11012-8", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1028815903"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/nar/gkh466", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1031671103"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/nar/gki918", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1031942595"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/nar/18.24.7213", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1032914011"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/nar/gkh450", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1034718853"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1146/annurev.biophys.32.110601.141800", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1035825525"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/1471-2105-6-190", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1038016276", 
          "https://doi.org/10.1186/1471-2105-6-190"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/1471-2105-6-190", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1038016276", 
          "https://doi.org/10.1186/1471-2105-6-190"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/s0097-8485(99)00007-8", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1038604376"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1371/journal.pone.0006441", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1040959990"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/bioinformatics/bth254", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1042719033"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1007/s001220051709", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1043289515", 
          "https://doi.org/10.1007/s001220051709"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1007/s001220051709", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1043289515", 
          "https://doi.org/10.1007/s001220051709"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1159/000084979", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1044099907"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1159/000084979", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1044099907"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/nar/6.11.3543", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1044432089"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/0888-7543(90)90166-r", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1045074026"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/1471-2105-13-134", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1046135038", 
          "https://doi.org/10.1186/1471-2105-13-134"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1021/bi962590c", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1055213079"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1021/bi962590c", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1055213079"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1021/bi9825091", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1055216937"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1021/bi9825091", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1055216937"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.3413476", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1062613076"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://app.dimensions.ai/details/publication/pub.1082984649", 
        "type": "CreativeWork"
      }
    ], 
    "datePublished": "2014", 
    "datePublishedReg": "2014-01-01", 
    "description": "This chapter introduces the software FastPCR as an integrated tools environment for PCR primer and probe design. It also predicts oligonucleotide properties based on experimental studies of PCR efficiency. The software provides comprehensive facilities for designing primers for most PCR applications and their combinations, including standard, multiplex, long-distance, inverse, real-time, group-specific, unique, and overlap extension PCR for multi-fragment assembly in cloning, as well as bisulphite modification assays. It includes a program to design oligonucleotide sets for long sequence assembly by the ligase chain reaction. The in silico PCR primer or probe search includes comprehensive analyses of individual primers and primer pairs. It calculates the melting temperature for standard and degenerate oligonucleotides including LNA and other modifications, provides analyses for a set of primers with prediction of oligonucleotide properties, dimer and G/C-quadruplex detection, and linguistic complexity, and provides a dilution and resuspension calculator. The program includes various bioinformatics tools for analysis of sequences with CG or AT skew, of CG content and purine-pyrimidine skew, and of linguistic sequence complexity. It also permits generation of random DNA sequence and analysis of restriction enzymes of all types. It finds or creates restriction enzyme recognition sites for coding sequences and supports the clustering of sequences. It generates consensus sequences and analyzes sequence conservation. It performs efficient and complete detection of various repeat types and displays them. FastPCR allows for sequence file batch processing, which is essential for automation. The FastPCR software is available for download at http://primerdigital.com/fastpcr.html and online version at http://primerdigital.com/tools/pcr.html . ", 
    "editor": [
      {
        "familyName": "Valla", 
        "givenName": "Svein", 
        "type": "Person"
      }, 
      {
        "familyName": "Lale", 
        "givenName": "Rahmi", 
        "type": "Person"
      }
    ], 
    "genre": "chapter", 
    "id": "sg:pub.10.1007/978-1-62703-764-8_18", 
    "inLanguage": [
      "en"
    ], 
    "isAccessibleForFree": true, 
    "isFundedItemOf": [
      {
        "id": "sg:grant.4250633", 
        "type": "MonetaryGrant"
      }
    ], 
    "isPartOf": {
      "isbn": [
        "978-1-62703-763-1", 
        "978-1-62703-764-8"
      ], 
      "name": "DNA Cloning and Assembly Methods", 
      "type": "Book"
    }, 
    "name": "FastPCR Software for PCR, In Silico PCR, and Oligonucleotide Assembly and Analysis", 
    "pagination": "271-302", 
    "productId": [
      {
        "name": "doi", 
        "type": "PropertyValue", 
        "value": [
          "10.1007/978-1-62703-764-8_18"
        ]
      }, 
      {
        "name": "readcube_id", 
        "type": "PropertyValue", 
        "value": [
          "cf2d6fbeaad87f382057d7e44a3ae41a3fdbde6cf5451bd2480a40cf4f5ed406"
        ]
      }, 
      {
        "name": "dimensions_id", 
        "type": "PropertyValue", 
        "value": [
          "pub.1043493906"
        ]
      }, 
      {
        "name": "pubmed_id", 
        "type": "PropertyValue", 
        "value": [
          "24395370"
        ]
      }
    ], 
    "publisher": {
      "location": "Totowa, NJ", 
      "name": "Humana Press", 
      "type": "Organisation"
    }, 
    "sameAs": [
      "https://doi.org/10.1007/978-1-62703-764-8_18", 
      "https://app.dimensions.ai/details/publication/pub.1043493906"
    ], 
    "sdDataset": "chapters", 
    "sdDatePublished": "2019-04-15T18:13", 
    "sdLicense": "https://scigraph.springernature.com/explorer/license/", 
    "sdPublisher": {
      "name": "Springer Nature - SN SciGraph project", 
      "type": "Organization"
    }, 
    "sdSource": "s3://com-uberresearch-data-dimensions-target-20181106-alternative/cleanup/v134/2549eaecd7973599484d7c17b260dba0a4ecb94b/merge/v9/a6c9fde33151104705d4d7ff012ea9563521a3ce/jats-lookup/v90/0000000001_0000000264/records_8681_00000270.jsonl", 
    "type": "Chapter", 
    "url": "http://link.springer.com/10.1007/978-1-62703-764-8_18"
  }
]
 

Download the RDF metadata as:  json-ld nt turtle xml License info

HOW TO GET THIS DATA PROGRAMMATICALLY:

JSON-LD is a popular format for linked data which is fully compatible with JSON.

curl -H 'Accept: application/ld+json' 'https://scigraph.springernature.com/pub.10.1007/978-1-62703-764-8_18'

N-Triples is a line-based linked data format ideal for batch operations.

curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1007/978-1-62703-764-8_18'

Turtle is a human-readable linked data format.

curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1007/978-1-62703-764-8_18'

RDF/XML is a standard XML format for linked data.

curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1007/978-1-62703-764-8_18'


 

This table displays all metadata directly associated to this object as RDF triples.

254 TRIPLES      23 PREDICATES      77 URIs      32 LITERALS      20 BLANK NODES

Subject Predicate Object
1 sg:pub.10.1007/978-1-62703-764-8_18 schema:about N0077d50458144a46a34c0eb86301232f
2 N254a5d683a5e4f93b85687a63e819419
3 N429205169dac43468be76915fe673de9
4 N8c6439ab4ba64d448fb1567d9918f6f2
5 N9ff8b23c64374ec9ab8462dd0fcf581e
6 Naedfcb3f9907436294479e1607243deb
7 Ne1a850877770471abf792c28480cca9b
8 Neb05b297e53c47d0a5e3a76435f53c85
9 Nf6644039a34b4d93912ccdc25f2613f8
10 Nfddf05d16901497a96dc357563495104
11 Nfe19f1d47b4347f9b8d96acf64a6e931
12 anzsrc-for:08
13 anzsrc-for:0802
14 schema:author N5698eaf0250143409af0f2a0aff03019
15 schema:citation sg:pub.10.1007/s001220051709
16 sg:pub.10.1038/nprot.2006.377
17 sg:pub.10.1186/1471-2105-13-134
18 sg:pub.10.1186/1471-2105-6-190
19 https://app.dimensions.ai/details/publication/pub.1082984649
20 https://doi.org/10.1016/0076-6879(92)11012-8
21 https://doi.org/10.1016/0888-7543(90)90166-r
22 https://doi.org/10.1016/j.ygeno.2011.04.009
23 https://doi.org/10.1016/s0006-3495(97)78756-3
24 https://doi.org/10.1016/s0097-8485(99)00007-8
25 https://doi.org/10.1021/bi962590c
26 https://doi.org/10.1021/bi9825091
27 https://doi.org/10.1073/pnas.48.8.1390
28 https://doi.org/10.1073/pnas.86.17.6686
29 https://doi.org/10.1073/pnas.91.20.9549
30 https://doi.org/10.1073/pnas.95.4.1460
31 https://doi.org/10.1093/bioinformatics/17.12.1226
32 https://doi.org/10.1093/bioinformatics/btg350
33 https://doi.org/10.1093/bioinformatics/bth254
34 https://doi.org/10.1093/bioinformatics/bti134
35 https://doi.org/10.1093/nar/18.22.6531
36 https://doi.org/10.1093/nar/18.24.7213
37 https://doi.org/10.1093/nar/24.18.3538
38 https://doi.org/10.1093/nar/28.9.1879
39 https://doi.org/10.1093/nar/30.3.e11
40 https://doi.org/10.1093/nar/6.11.3543
41 https://doi.org/10.1093/nar/gkh450
42 https://doi.org/10.1093/nar/gkh466
43 https://doi.org/10.1093/nar/gki918
44 https://doi.org/10.1093/nar/gkn191
45 https://doi.org/10.1093/nar/gkn198
46 https://doi.org/10.1093/nar/gkp026
47 https://doi.org/10.1093/nar/gkq639
48 https://doi.org/10.1093/nar/gks596
49 https://doi.org/10.1126/science.3413476
50 https://doi.org/10.1146/annurev.biophys.32.110601.141800
51 https://doi.org/10.1159/000084979
52 https://doi.org/10.1371/journal.pone.0006441
53 schema:datePublished 2014
54 schema:datePublishedReg 2014-01-01
55 schema:description This chapter introduces the software FastPCR as an integrated tools environment for PCR primer and probe design. It also predicts oligonucleotide properties based on experimental studies of PCR efficiency. The software provides comprehensive facilities for designing primers for most PCR applications and their combinations, including standard, multiplex, long-distance, inverse, real-time, group-specific, unique, and overlap extension PCR for multi-fragment assembly in cloning, as well as bisulphite modification assays. It includes a program to design oligonucleotide sets for long sequence assembly by the ligase chain reaction. The in silico PCR primer or probe search includes comprehensive analyses of individual primers and primer pairs. It calculates the melting temperature for standard and degenerate oligonucleotides including LNA and other modifications, provides analyses for a set of primers with prediction of oligonucleotide properties, dimer and G/C-quadruplex detection, and linguistic complexity, and provides a dilution and resuspension calculator. The program includes various bioinformatics tools for analysis of sequences with CG or AT skew, of CG content and purine-pyrimidine skew, and of linguistic sequence complexity. It also permits generation of random DNA sequence and analysis of restriction enzymes of all types. It finds or creates restriction enzyme recognition sites for coding sequences and supports the clustering of sequences. It generates consensus sequences and analyzes sequence conservation. It performs efficient and complete detection of various repeat types and displays them. FastPCR allows for sequence file batch processing, which is essential for automation. The FastPCR software is available for download at http://primerdigital.com/fastpcr.html and online version at http://primerdigital.com/tools/pcr.html .
56 schema:editor Nb00dba8343a945778de783201c98af5a
57 schema:genre chapter
58 schema:inLanguage en
59 schema:isAccessibleForFree true
60 schema:isPartOf Nc6089fd864ab44f78818b91e8cd17898
61 schema:name FastPCR Software for PCR, In Silico PCR, and Oligonucleotide Assembly and Analysis
62 schema:pagination 271-302
63 schema:productId N9ebb4eb8c78741b986ed26370c370c6f
64 Na989ec476c95435ca75a6700328f4ffb
65 Nd7afb498de164a7fa4dea7fc5f16dc00
66 Nfed41532633d4117865043d8257f971c
67 schema:publisher N62afb8cf73214bdda59f9f2feeb074ef
68 schema:sameAs https://app.dimensions.ai/details/publication/pub.1043493906
69 https://doi.org/10.1007/978-1-62703-764-8_18
70 schema:sdDatePublished 2019-04-15T18:13
71 schema:sdLicense https://scigraph.springernature.com/explorer/license/
72 schema:sdPublisher N3a7c61cf9ee642be8c9ce162a7de95ac
73 schema:url http://link.springer.com/10.1007/978-1-62703-764-8_18
74 sgo:license sg:explorer/license/
75 sgo:sdDataset chapters
76 rdf:type schema:Chapter
77 N0077d50458144a46a34c0eb86301232f schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
78 schema:name Inverted Repeat Sequences
79 rdf:type schema:DefinedTerm
80 N1adc259c54dc4ec18261d2091976cad4 schema:familyName Valla
81 schema:givenName Svein
82 rdf:type schema:Person
83 N254a5d683a5e4f93b85687a63e819419 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
84 schema:name Nucleic Acid Denaturation
85 rdf:type schema:DefinedTerm
86 N3a7c61cf9ee642be8c9ce162a7de95ac schema:name Springer Nature - SN SciGraph project
87 rdf:type schema:Organization
88 N429205169dac43468be76915fe673de9 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
89 schema:name Sequence Analysis, DNA
90 rdf:type schema:DefinedTerm
91 N4c017475d5b54a65ab76e72fd6f5db00 rdf:first N6f341c4be4fb4ad4973c566033423f4d
92 rdf:rest rdf:nil
93 N5698eaf0250143409af0f2a0aff03019 rdf:first sg:person.01061032627.62
94 rdf:rest N5b2fc84b0c734a14a12cc04217540d51
95 N5b2fc84b0c734a14a12cc04217540d51 rdf:first sg:person.01303225202.04
96 rdf:rest N603994cbea144993bc2f16f9abc9fb47
97 N603994cbea144993bc2f16f9abc9fb47 rdf:first sg:person.0777404667.23
98 rdf:rest rdf:nil
99 N62afb8cf73214bdda59f9f2feeb074ef schema:location Totowa, NJ
100 schema:name Humana Press
101 rdf:type schema:Organisation
102 N6f341c4be4fb4ad4973c566033423f4d schema:familyName Lale
103 schema:givenName Rahmi
104 rdf:type schema:Person
105 N8c6439ab4ba64d448fb1567d9918f6f2 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
106 schema:name Computer Simulation
107 rdf:type schema:DefinedTerm
108 N9ebb4eb8c78741b986ed26370c370c6f schema:name dimensions_id
109 schema:value pub.1043493906
110 rdf:type schema:PropertyValue
111 N9ff8b23c64374ec9ab8462dd0fcf581e schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
112 schema:name Oligonucleotides
113 rdf:type schema:DefinedTerm
114 Na989ec476c95435ca75a6700328f4ffb schema:name readcube_id
115 schema:value cf2d6fbeaad87f382057d7e44a3ae41a3fdbde6cf5451bd2480a40cf4f5ed406
116 rdf:type schema:PropertyValue
117 Naedfcb3f9907436294479e1607243deb schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
118 schema:name Polymerase Chain Reaction
119 rdf:type schema:DefinedTerm
120 Nb00dba8343a945778de783201c98af5a rdf:first N1adc259c54dc4ec18261d2091976cad4
121 rdf:rest N4c017475d5b54a65ab76e72fd6f5db00
122 Nc6089fd864ab44f78818b91e8cd17898 schema:isbn 978-1-62703-763-1
123 978-1-62703-764-8
124 schema:name DNA Cloning and Assembly Methods
125 rdf:type schema:Book
126 Nd7afb498de164a7fa4dea7fc5f16dc00 schema:name pubmed_id
127 schema:value 24395370
128 rdf:type schema:PropertyValue
129 Ne1a850877770471abf792c28480cca9b schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
130 schema:name DNA Primers
131 rdf:type schema:DefinedTerm
132 Neb05b297e53c47d0a5e3a76435f53c85 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
133 schema:name Software
134 rdf:type schema:DefinedTerm
135 Nf6644039a34b4d93912ccdc25f2613f8 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
136 schema:name Transition Temperature
137 rdf:type schema:DefinedTerm
138 Nfddf05d16901497a96dc357563495104 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
139 schema:name Time Factors
140 rdf:type schema:DefinedTerm
141 Nfe19f1d47b4347f9b8d96acf64a6e931 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
142 schema:name Microsatellite Repeats
143 rdf:type schema:DefinedTerm
144 Nfed41532633d4117865043d8257f971c schema:name doi
145 schema:value 10.1007/978-1-62703-764-8_18
146 rdf:type schema:PropertyValue
147 anzsrc-for:08 schema:inDefinedTermSet anzsrc-for:
148 schema:name Information and Computing Sciences
149 rdf:type schema:DefinedTerm
150 anzsrc-for:0802 schema:inDefinedTermSet anzsrc-for:
151 schema:name Computation Theory and Mathematics
152 rdf:type schema:DefinedTerm
153 sg:grant.4250633 http://pending.schema.org/fundedItem sg:pub.10.1007/978-1-62703-764-8_18
154 rdf:type schema:MonetaryGrant
155 sg:person.01061032627.62 schema:affiliation https://www.grid.ac/institutes/grid.7737.4
156 schema:familyName Kalendar
157 schema:givenName Ruslan
158 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01061032627.62
159 rdf:type schema:Person
160 sg:person.01303225202.04 schema:affiliation https://www.grid.ac/institutes/grid.17595.3f
161 schema:familyName Lee
162 schema:givenName David
163 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01303225202.04
164 rdf:type schema:Person
165 sg:person.0777404667.23 schema:affiliation https://www.grid.ac/institutes/grid.7737.4
166 schema:familyName Schulman
167 schema:givenName Alan H.
168 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0777404667.23
169 rdf:type schema:Person
170 sg:pub.10.1007/s001220051709 schema:sameAs https://app.dimensions.ai/details/publication/pub.1043289515
171 https://doi.org/10.1007/s001220051709
172 rdf:type schema:CreativeWork
173 sg:pub.10.1038/nprot.2006.377 schema:sameAs https://app.dimensions.ai/details/publication/pub.1015945679
174 https://doi.org/10.1038/nprot.2006.377
175 rdf:type schema:CreativeWork
176 sg:pub.10.1186/1471-2105-13-134 schema:sameAs https://app.dimensions.ai/details/publication/pub.1046135038
177 https://doi.org/10.1186/1471-2105-13-134
178 rdf:type schema:CreativeWork
179 sg:pub.10.1186/1471-2105-6-190 schema:sameAs https://app.dimensions.ai/details/publication/pub.1038016276
180 https://doi.org/10.1186/1471-2105-6-190
181 rdf:type schema:CreativeWork
182 https://app.dimensions.ai/details/publication/pub.1082984649 schema:CreativeWork
183 https://doi.org/10.1016/0076-6879(92)11012-8 schema:sameAs https://app.dimensions.ai/details/publication/pub.1028815903
184 rdf:type schema:CreativeWork
185 https://doi.org/10.1016/0888-7543(90)90166-r schema:sameAs https://app.dimensions.ai/details/publication/pub.1045074026
186 rdf:type schema:CreativeWork
187 https://doi.org/10.1016/j.ygeno.2011.04.009 schema:sameAs https://app.dimensions.ai/details/publication/pub.1018579651
188 rdf:type schema:CreativeWork
189 https://doi.org/10.1016/s0006-3495(97)78756-3 schema:sameAs https://app.dimensions.ai/details/publication/pub.1027176605
190 rdf:type schema:CreativeWork
191 https://doi.org/10.1016/s0097-8485(99)00007-8 schema:sameAs https://app.dimensions.ai/details/publication/pub.1038604376
192 rdf:type schema:CreativeWork
193 https://doi.org/10.1021/bi962590c schema:sameAs https://app.dimensions.ai/details/publication/pub.1055213079
194 rdf:type schema:CreativeWork
195 https://doi.org/10.1021/bi9825091 schema:sameAs https://app.dimensions.ai/details/publication/pub.1055216937
196 rdf:type schema:CreativeWork
197 https://doi.org/10.1073/pnas.48.8.1390 schema:sameAs https://app.dimensions.ai/details/publication/pub.1011693507
198 rdf:type schema:CreativeWork
199 https://doi.org/10.1073/pnas.86.17.6686 schema:sameAs https://app.dimensions.ai/details/publication/pub.1019941969
200 rdf:type schema:CreativeWork
201 https://doi.org/10.1073/pnas.91.20.9549 schema:sameAs https://app.dimensions.ai/details/publication/pub.1014181108
202 rdf:type schema:CreativeWork
203 https://doi.org/10.1073/pnas.95.4.1460 schema:sameAs https://app.dimensions.ai/details/publication/pub.1009187647
204 rdf:type schema:CreativeWork
205 https://doi.org/10.1093/bioinformatics/17.12.1226 schema:sameAs https://app.dimensions.ai/details/publication/pub.1014919468
206 rdf:type schema:CreativeWork
207 https://doi.org/10.1093/bioinformatics/btg350 schema:sameAs https://app.dimensions.ai/details/publication/pub.1012323448
208 rdf:type schema:CreativeWork
209 https://doi.org/10.1093/bioinformatics/bth254 schema:sameAs https://app.dimensions.ai/details/publication/pub.1042719033
210 rdf:type schema:CreativeWork
211 https://doi.org/10.1093/bioinformatics/bti134 schema:sameAs https://app.dimensions.ai/details/publication/pub.1006446393
212 rdf:type schema:CreativeWork
213 https://doi.org/10.1093/nar/18.22.6531 schema:sameAs https://app.dimensions.ai/details/publication/pub.1022940325
214 rdf:type schema:CreativeWork
215 https://doi.org/10.1093/nar/18.24.7213 schema:sameAs https://app.dimensions.ai/details/publication/pub.1032914011
216 rdf:type schema:CreativeWork
217 https://doi.org/10.1093/nar/24.18.3538 schema:sameAs https://app.dimensions.ai/details/publication/pub.1019513958
218 rdf:type schema:CreativeWork
219 https://doi.org/10.1093/nar/28.9.1879 schema:sameAs https://app.dimensions.ai/details/publication/pub.1003733221
220 rdf:type schema:CreativeWork
221 https://doi.org/10.1093/nar/30.3.e11 schema:sameAs https://app.dimensions.ai/details/publication/pub.1018841621
222 rdf:type schema:CreativeWork
223 https://doi.org/10.1093/nar/6.11.3543 schema:sameAs https://app.dimensions.ai/details/publication/pub.1044432089
224 rdf:type schema:CreativeWork
225 https://doi.org/10.1093/nar/gkh450 schema:sameAs https://app.dimensions.ai/details/publication/pub.1034718853
226 rdf:type schema:CreativeWork
227 https://doi.org/10.1093/nar/gkh466 schema:sameAs https://app.dimensions.ai/details/publication/pub.1031671103
228 rdf:type schema:CreativeWork
229 https://doi.org/10.1093/nar/gki918 schema:sameAs https://app.dimensions.ai/details/publication/pub.1031942595
230 rdf:type schema:CreativeWork
231 https://doi.org/10.1093/nar/gkn191 schema:sameAs https://app.dimensions.ai/details/publication/pub.1027671874
232 rdf:type schema:CreativeWork
233 https://doi.org/10.1093/nar/gkn198 schema:sameAs https://app.dimensions.ai/details/publication/pub.1006730464
234 rdf:type schema:CreativeWork
235 https://doi.org/10.1093/nar/gkp026 schema:sameAs https://app.dimensions.ai/details/publication/pub.1006892534
236 rdf:type schema:CreativeWork
237 https://doi.org/10.1093/nar/gkq639 schema:sameAs https://app.dimensions.ai/details/publication/pub.1016305635
238 rdf:type schema:CreativeWork
239 https://doi.org/10.1093/nar/gks596 schema:sameAs https://app.dimensions.ai/details/publication/pub.1014785724
240 rdf:type schema:CreativeWork
241 https://doi.org/10.1126/science.3413476 schema:sameAs https://app.dimensions.ai/details/publication/pub.1062613076
242 rdf:type schema:CreativeWork
243 https://doi.org/10.1146/annurev.biophys.32.110601.141800 schema:sameAs https://app.dimensions.ai/details/publication/pub.1035825525
244 rdf:type schema:CreativeWork
245 https://doi.org/10.1159/000084979 schema:sameAs https://app.dimensions.ai/details/publication/pub.1044099907
246 rdf:type schema:CreativeWork
247 https://doi.org/10.1371/journal.pone.0006441 schema:sameAs https://app.dimensions.ai/details/publication/pub.1040959990
248 rdf:type schema:CreativeWork
249 https://www.grid.ac/institutes/grid.17595.3f schema:alternateName National Institute of Agricultural Botany
250 schema:name John Bingham Laboratory, National Institute of Agricultural Botany, Cambridge, UK
251 rdf:type schema:Organization
252 https://www.grid.ac/institutes/grid.7737.4 schema:alternateName University of Helsinki
253 schema:name MTT/BI Plant Genomics Laboratory, Institute of Biotechnology, University of Helsinki, Helsinki, Finland
254 rdf:type schema:Organization
 




Preview window. Press ESC to close (or click here)


...