PathoGene TM

A CDS Finding and Primer Design Tool for Microorganisms


  Input

Please visit PathoGene DB for pre-computed primers to entire genomes under default parameters

Choose organism:
Bacteria:
Virus:
Fungi:
NIH Categorized Agents:
CDC Categorized Agents:
Choose locating method:
GenBank Annotation
TIGR Glimmer v2.13 Glimmer options:
Find CDS by:
Number CDS:
Gene Name (Annotation only)
Locus Tag (Annotation only)

OR

Enter a FASTA format sequence:
 These symbols should NOT be used in the comments field: ` # $ % & ( ) \ | ; ' " < > / ?
or upload a FASTA format file (PLAIN-TEXT only):





  Primer Picking Parameters

No.to Return: Max 3' Stability:
Max Mispriming: Pair Max Mispriming:
Product Size Min: Opt: Max:
Primer Size Min: Opt: Max:
Primer Tm Min: Opt: Max:
Primer GC% Min: Opt: Max:
Max Self Complementarity: Max 3' Self Complementarity:
Max #N's: Max Poly-X:
CG Clamp: Max Tm Difference:
Generate Internal Primers Generate RT-PCR primers


  Sequence Options

Split CDS > 500 bp

Find upstream "promoter" region and design primers

Find 2 kbp upstream region and design primers

Flanking sequence for CDS: nucleotides

Buffer sequence between primer and CDS: nucleotides


  BLAST Options

BLAST PCR product against selected genome

BLAST primers against selected genome

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A service of the RCE Region VI Computational Biology Group. Email errors or comments to PathoGene Tech Support
Copyright © 2003 UT Southwestern Medical Center and RCE Region VI Computational Biology Group. All rights reserved.