AutoPrime: selecting primers for expressed sequences View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2004-05

AUTHORS

Gunnar Wrobel, Felix Kokocinski, Peter Lichter

ABSTRACT

Primers designed for expressed sequences should be specific for the mRNA sequence of a gene but not yield a product from its genomic sequence. Already slight contaminations of genomic DNA can lead to incorrect measurements for sensitive methods like real-time PCR (RT-PCR). The software AutoPrime automates the task of generating such primers for RT-PCR experiments by combining the information from sequence databases with primer design software. Thus the software is able to cope with the high demand of RT-PCR validation experiments following the recent increase in microarray expression profiling studies. The software generates high quality primers more efficiently than possible by manual design methods and has been successfully employed for RT-PCR primer design in our as well as other laboratories. More... »

PAGES

p11

References to SciGraph publications

  • 1999-08-26. Primer3 on the WWW for General Users and for Biologist Programmers in BIOINFORMATICS METHODS AND PROTOCOLS
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1186/gb-2004-5-5-p11

    DOI

    http://dx.doi.org/10.1186/gb-2004-5-5-p11

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1004632209


    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/2008/0604", 
            "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
            "name": "Genetics", 
            "type": "DefinedTerm"
          }, 
          {
            "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/06", 
            "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
            "name": "Biological Sciences", 
            "type": "DefinedTerm"
          }
        ], 
        "author": [
          {
            "affiliation": {
              "alternateName": "Swiss Institute of Bioinformatics", 
              "id": "https://www.grid.ac/institutes/grid.419765.8", 
              "name": [
                "Divisions of Bioinformatics and Biochemistry, Swiss Institute of Bioinformatics, Klingelbergstrasse 50/70, 4056, Basel, Switzerland"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Wrobel", 
            "givenName": "Gunnar", 
            "id": "sg:person.01247575476.50", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01247575476.50"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "German Cancer Research Center", 
              "id": "https://www.grid.ac/institutes/grid.7497.d", 
              "name": [
                "Molecular Genetics, Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 280, 69120, Heidelberg, Germany"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Kokocinski", 
            "givenName": "Felix", 
            "id": "sg:person.0637153667.93", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0637153667.93"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "German Cancer Research Center", 
              "id": "https://www.grid.ac/institutes/grid.7497.d", 
              "name": [
                "Molecular Genetics, Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 280, 69120, Heidelberg, Germany"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Lichter", 
            "givenName": "Peter", 
            "id": "sg:person.01243467607.83", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01243467607.83"
            ], 
            "type": "Person"
          }
        ], 
        "citation": [
          {
            "id": "https://doi.org/10.1093/nar/gkg011", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1009194731"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1093/nar/26.12.3006", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1013270498"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1385/1-59259-192-2:365", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1023668922", 
              "https://doi.org/10.1385/1-59259-192-2:365"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1093/bioinformatics/17.1.98", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1025655527"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1101/gr.361602", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1028020859"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1093/nar/gng154", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1034241213"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1016/s0168-9525(00)02093-x", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1040981053"
            ], 
            "type": "CreativeWork"
          }
        ], 
        "datePublished": "2004-05", 
        "datePublishedReg": "2004-05-01", 
        "description": "Primers designed for expressed sequences should be specific for the mRNA sequence of a gene but not yield a product from its genomic sequence. Already slight contaminations of genomic DNA can lead to incorrect measurements for sensitive methods like real-time PCR (RT-PCR). The software AutoPrime automates the task of generating such primers for RT-PCR experiments by combining the information from sequence databases with primer design software. Thus the software is able to cope with the high demand of RT-PCR validation experiments following the recent increase in microarray expression profiling studies. The software generates high quality primers more efficiently than possible by manual design methods and has been successfully employed for RT-PCR primer design in our as well as other laboratories.", 
        "genre": "non_research_article", 
        "id": "sg:pub.10.1186/gb-2004-5-5-p11", 
        "inLanguage": [
          "en"
        ], 
        "isAccessibleForFree": true, 
        "isPartOf": [
          {
            "id": "sg:journal.1023439", 
            "issn": [
              "1474-760X", 
              "1465-6906"
            ], 
            "name": "Genome Biology", 
            "type": "Periodical"
          }, 
          {
            "issueNumber": "5", 
            "type": "PublicationIssue"
          }, 
          {
            "type": "PublicationVolume", 
            "volumeNumber": "5"
          }
        ], 
        "name": "AutoPrime: selecting primers for expressed sequences", 
        "pagination": "p11", 
        "productId": [
          {
            "name": "readcube_id", 
            "type": "PropertyValue", 
            "value": [
              "16128024ec380f27527e2a2b453a765a7b404393b833e96c3a0bbc04cd159a29"
            ]
          }, 
          {
            "name": "doi", 
            "type": "PropertyValue", 
            "value": [
              "10.1186/gb-2004-5-5-p11"
            ]
          }, 
          {
            "name": "dimensions_id", 
            "type": "PropertyValue", 
            "value": [
              "pub.1004632209"
            ]
          }
        ], 
        "sameAs": [
          "https://doi.org/10.1186/gb-2004-5-5-p11", 
          "https://app.dimensions.ai/details/publication/pub.1004632209"
        ], 
        "sdDataset": "articles", 
        "sdDatePublished": "2019-04-10T17:31", 
        "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_8672_00000510.jsonl", 
        "type": "ScholarlyArticle", 
        "url": "http://link.springer.com/10.1186%2Fgb-2004-5-5-p11"
      }
    ]
     

    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.10.1186/gb-2004-5-5-p11'

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

    curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1186/gb-2004-5-5-p11'

    Turtle is a human-readable linked data format.

    curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1186/gb-2004-5-5-p11'

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

    curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1186/gb-2004-5-5-p11'


     

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

    100 TRIPLES      21 PREDICATES      34 URIs      19 LITERALS      7 BLANK NODES

    Subject Predicate Object
    1 sg:pub.10.1186/gb-2004-5-5-p11 schema:about anzsrc-for:06
    2 anzsrc-for:0604
    3 schema:author N3ce5250d6c2341ea84e76b4b1eca0ca2
    4 schema:citation sg:pub.10.1385/1-59259-192-2:365
    5 https://doi.org/10.1016/s0168-9525(00)02093-x
    6 https://doi.org/10.1093/bioinformatics/17.1.98
    7 https://doi.org/10.1093/nar/26.12.3006
    8 https://doi.org/10.1093/nar/gkg011
    9 https://doi.org/10.1093/nar/gng154
    10 https://doi.org/10.1101/gr.361602
    11 schema:datePublished 2004-05
    12 schema:datePublishedReg 2004-05-01
    13 schema:description Primers designed for expressed sequences should be specific for the mRNA sequence of a gene but not yield a product from its genomic sequence. Already slight contaminations of genomic DNA can lead to incorrect measurements for sensitive methods like real-time PCR (RT-PCR). The software AutoPrime automates the task of generating such primers for RT-PCR experiments by combining the information from sequence databases with primer design software. Thus the software is able to cope with the high demand of RT-PCR validation experiments following the recent increase in microarray expression profiling studies. The software generates high quality primers more efficiently than possible by manual design methods and has been successfully employed for RT-PCR primer design in our as well as other laboratories.
    14 schema:genre non_research_article
    15 schema:inLanguage en
    16 schema:isAccessibleForFree true
    17 schema:isPartOf N1714eee2dbe645568e0a740baa3475db
    18 Nb9d67d0637c44ac99b175fe2d9be0f3c
    19 sg:journal.1023439
    20 schema:name AutoPrime: selecting primers for expressed sequences
    21 schema:pagination p11
    22 schema:productId N9f9b0e90f64a43c7b4619c24705270d9
    23 Nca33cd000bde4a00a1edb7a94bd9729e
    24 Nf3f9338ed0bb4c2da3cf1199ce437cc6
    25 schema:sameAs https://app.dimensions.ai/details/publication/pub.1004632209
    26 https://doi.org/10.1186/gb-2004-5-5-p11
    27 schema:sdDatePublished 2019-04-10T17:31
    28 schema:sdLicense https://scigraph.springernature.com/explorer/license/
    29 schema:sdPublisher Nb41107fdeeb046c69198badd07d72505
    30 schema:url http://link.springer.com/10.1186%2Fgb-2004-5-5-p11
    31 sgo:license sg:explorer/license/
    32 sgo:sdDataset articles
    33 rdf:type schema:ScholarlyArticle
    34 N1714eee2dbe645568e0a740baa3475db schema:volumeNumber 5
    35 rdf:type schema:PublicationVolume
    36 N2cddddec95d24cb48084da53b96ff697 rdf:first sg:person.0637153667.93
    37 rdf:rest N7e260911d5ea45afa2102e28fef56d52
    38 N3ce5250d6c2341ea84e76b4b1eca0ca2 rdf:first sg:person.01247575476.50
    39 rdf:rest N2cddddec95d24cb48084da53b96ff697
    40 N7e260911d5ea45afa2102e28fef56d52 rdf:first sg:person.01243467607.83
    41 rdf:rest rdf:nil
    42 N9f9b0e90f64a43c7b4619c24705270d9 schema:name readcube_id
    43 schema:value 16128024ec380f27527e2a2b453a765a7b404393b833e96c3a0bbc04cd159a29
    44 rdf:type schema:PropertyValue
    45 Nb41107fdeeb046c69198badd07d72505 schema:name Springer Nature - SN SciGraph project
    46 rdf:type schema:Organization
    47 Nb9d67d0637c44ac99b175fe2d9be0f3c schema:issueNumber 5
    48 rdf:type schema:PublicationIssue
    49 Nca33cd000bde4a00a1edb7a94bd9729e schema:name doi
    50 schema:value 10.1186/gb-2004-5-5-p11
    51 rdf:type schema:PropertyValue
    52 Nf3f9338ed0bb4c2da3cf1199ce437cc6 schema:name dimensions_id
    53 schema:value pub.1004632209
    54 rdf:type schema:PropertyValue
    55 anzsrc-for:06 schema:inDefinedTermSet anzsrc-for:
    56 schema:name Biological Sciences
    57 rdf:type schema:DefinedTerm
    58 anzsrc-for:0604 schema:inDefinedTermSet anzsrc-for:
    59 schema:name Genetics
    60 rdf:type schema:DefinedTerm
    61 sg:journal.1023439 schema:issn 1465-6906
    62 1474-760X
    63 schema:name Genome Biology
    64 rdf:type schema:Periodical
    65 sg:person.01243467607.83 schema:affiliation https://www.grid.ac/institutes/grid.7497.d
    66 schema:familyName Lichter
    67 schema:givenName Peter
    68 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01243467607.83
    69 rdf:type schema:Person
    70 sg:person.01247575476.50 schema:affiliation https://www.grid.ac/institutes/grid.419765.8
    71 schema:familyName Wrobel
    72 schema:givenName Gunnar
    73 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01247575476.50
    74 rdf:type schema:Person
    75 sg:person.0637153667.93 schema:affiliation https://www.grid.ac/institutes/grid.7497.d
    76 schema:familyName Kokocinski
    77 schema:givenName Felix
    78 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0637153667.93
    79 rdf:type schema:Person
    80 sg:pub.10.1385/1-59259-192-2:365 schema:sameAs https://app.dimensions.ai/details/publication/pub.1023668922
    81 https://doi.org/10.1385/1-59259-192-2:365
    82 rdf:type schema:CreativeWork
    83 https://doi.org/10.1016/s0168-9525(00)02093-x schema:sameAs https://app.dimensions.ai/details/publication/pub.1040981053
    84 rdf:type schema:CreativeWork
    85 https://doi.org/10.1093/bioinformatics/17.1.98 schema:sameAs https://app.dimensions.ai/details/publication/pub.1025655527
    86 rdf:type schema:CreativeWork
    87 https://doi.org/10.1093/nar/26.12.3006 schema:sameAs https://app.dimensions.ai/details/publication/pub.1013270498
    88 rdf:type schema:CreativeWork
    89 https://doi.org/10.1093/nar/gkg011 schema:sameAs https://app.dimensions.ai/details/publication/pub.1009194731
    90 rdf:type schema:CreativeWork
    91 https://doi.org/10.1093/nar/gng154 schema:sameAs https://app.dimensions.ai/details/publication/pub.1034241213
    92 rdf:type schema:CreativeWork
    93 https://doi.org/10.1101/gr.361602 schema:sameAs https://app.dimensions.ai/details/publication/pub.1028020859
    94 rdf:type schema:CreativeWork
    95 https://www.grid.ac/institutes/grid.419765.8 schema:alternateName Swiss Institute of Bioinformatics
    96 schema:name Divisions of Bioinformatics and Biochemistry, Swiss Institute of Bioinformatics, Klingelbergstrasse 50/70, 4056, Basel, Switzerland
    97 rdf:type schema:Organization
    98 https://www.grid.ac/institutes/grid.7497.d schema:alternateName German Cancer Research Center
    99 schema:name Molecular Genetics, Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
    100 rdf:type schema:Organization
     




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


    ...