A tool aligning 2 homolog sequences to design primers on the consensus sequence
INTRODUCTION
This is the input interface for the "PRIM2" tool (version 0.5), an experimental program developed in perl that bundle togather the NCBI "Blast2" and MIT "Primer3" programs for a streamlined primer design based on sequence homologies. Codes are also developed to show consensus sequences aligned with the raw homologous sequences, and to mask out the part that do not have good homology matches therefore the primer design will avoid these regions.

USAGE
Paste sequences in the windows below (if the sequences are in FASTA format the sequence names will be shown in the alignment; if they are only plain sequences, the program will assign names "Sequence 1" and "Sequence 2" to them respectively):

Primer design parameters:
Minimum Tm:
Optimum Tm:
Maximum Tm: 		Maximum primer size:
PCR product size:
Maximum GC content:
Number of primers to design:
Number of "N"s acceptable:
Homologous Sequence 1:
Homologous Sequence 2:

THIRD PARTY SOFTWARE:
Two 3rd party software are embeded:

  1. BLAST2: To align 2 homologous sequences from which a consensus may be derived.
    • Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman, (1997). Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Res. 25:3389-3402.
  2. Primer3 Program: Used to design primers on the consensus sequence formed.
    • Rozen, S., Skaletsky, H. "Primer3 on the WWW for general users and for biologist programmers." In S. Krawetz and S. Misener, eds. Bioinformatics Methods and Protocols in the series Methods in Molecular Biology. Humana Press, Totowa, NJ, 2000, pages 365-386.

ACKNOWLEDGEMENTS:
Thanks are due to Kwan-Suk Kim for useful discussions. This work is supported by funds from the USDA National Animal Genome Research Program, Pig Genome Coordination and Bioinformatics Coordination Programs.

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