Skip to content

GetPrimers web application manual

Jump to bottom
Zepu Miao edited this page Nov 3, 2023 · 5 revisions

Introduction

GetPrimers's web interface can be accessed via https://www.evomicslab.org/app/getprimers/. Through a browser users can query or de novo design gene targeting primers for a pre-shipped strain. Users can also upload customized genome, annotation and gene targeting cassette files to design gene targeting primers. But if the genome size is too large it may take a long time to get the results. It’s recommended to design primers for a strain with >20M genome size by installing and running GetPrimers locally.

  • Pre-built database
species strain
Schizosaccharomyces pombe 972h
Schizosaccharomyces cryophilus OY26
Schizosaccharomyces japonicus yFS275
Schizosaccharomyces octosporus yFS286
Saccharomyces cerevisiae S288C, DBVPG6044, DBVPG6765, SK1, Y12, YPS128, UWOPS03-461.4
Schizosaccharomyces cryophilus OY26
Schizosaccharomyces japonicus yFS275
Schizosaccharomyces octosporus yFS286
Schizosaccharomyces osmophilus CBS15793T
Neurospora crassa OR74A
Fusarium oxysporum f.sp.lycopersici 4287
Verticillium dahliae VdLs.17
Sporisorium scitamineum SSC39B
Pyricularia oryzae 70-15
  • Home page

Home page of web site

Example

  • Choose the assembly

Home page of web site

  • Choose the plasmid

Choose the plasmid

  • Fill in the gene list

Fill in the gene list

  • Choose the strategy

Choose the strategy

  • Choose the primer type

Choose the primer type

  • Modify parameters

Modify parameters

  • Submit and save the results

Submit and save the results

Notes

Upload assembly and GFF

If users want to design gene targeting primers by using customized assembly or annotation both of these two files should be uploaded. In regard to annotation file that downloaded from NCBI or Ensembl in the GFF format is preferred and that from other source may cause unpredictable error. Users should transform the annotation file to NCBI or Ensembl style if needed.

Choose a pre-built plasmid cassette and Primer type

Please choose the plasmid cassette and primer type carefully. For example, a C’ tagging plasmid and N’ tagging primer type will cause incorrect results.

Gene list

Can be a single gene or a gene list. Gene name, gene ID and Dbxref ID are all supported for NCBI GFF. Dbxref ID are not supported for Ensembl GFF.

  • Annotation ID List:

    YAL067C
    YAL064C-A

  • Gene Name List:

    SEO1
    TDA8

  • Dbxref ID List:

    851230
    851234

Primer location

Commonly, parts of G3, G4, P1 and P2 that are homologous to plasmid are not needed to be redesigned. The length of the part can be assigned. By default, this value is 20. If users want to redesign this part by melt temperature, bases composition and other criteria please select the check box ‘redesign primer common sequence, which is homologous to insertion cassette’ in ‘Other options’. By this option V5 and V6 are also redesigned.

Verification primers

By default, verification primers V5 and V6 are complementary to parts of G3, G4, P1 and P2 that are homologous to plasmid.

Repeat masking

The function of 'repeat masking' is to keep the 3' end of primers away from the template region enriched of repeat sequence. The 'repeat masking' option under 'Other options' is turned on by default.

Blast

Electronical PCR is implemented based on 'blast'. By default, the 'blast' option under 'Other options' is turned on.

Schematic and output information

Please read https://www.evomicslab.org/app/getprimers/info/

Clone this wiki locally