Tutorial in English

Tutorial in Chinese

There are four routes can be performed in UPS 2.0.

routes of UPS

arrowOption Unique Probe within group is used to select the best, most unique probe for each sequence to match its target but will not hybridize to all the other submitted sequences.

Scenarios for this option: PCR fragments (amplified by common primer pairs), a set of sequences for probe design for small array/hybridization use.

Application Scenario 1: A bundle of PCR products amplified by common primers from several pathogens as input was performed in UPS with the option of Unique probe within group, we can design a small probe set to generate a small array to discriminate each pathogen from clinical samples or contaminants.

 

arrowOption Unique Probe in the specific organism is to devise probes for each submitted sequence to identify its target among the selected genetic background based on Unigene.

Scenarios for this option: Pathogen detective and diagnostic kits development (using pathogen sequences for probe design under consideration of  host genetic background), a set of sequences in specific organism for unique probe design for hybridization use.

Scenario 2: If we want to design a probe for detection of specific pathogen from specimen of particular organism (human in this case), we can use those sequences from pathogen as input with the option, Unique Probe in specific organism, and select Mus_musculus (Mouse) from menu. Then the system will help us to sketch the suitable probe set for identify specific pathogen without the conflict of genetic background from specimen.

arrowOption Unique Probe based on pangenomic level is to customize the probe design among environmental and non-redundant nucleotide sequences on the level of pangenomics.

arrowOption Unique Probe based on user's defined organism is to allows users to upload a set of sequences or genomes in fasta format as the reference genetic background for probe design.

Scenarios for this option: Pathogen detective and diagnostic kits development (using pathogen sequences for probe design under consideration of  host genetic background (by "user-defined" uploaded sequences)), a set of sequences in "user-defined" organism for unique probe design for hybridization use. The submitted genome should be in fasta format.

Scenario 3: If we want to design a probe for detection of specific pathogen from specimen of particular organism (not listed in Unigene, they may be found in NCBI genome FTP), we can use those sequences from pathogen as input with the option, Unique Probe in specific organism, and uploaduser-defined genome/sequences . Then the system will help us to sketch the suitable probe set for identify specific pathogen without the conflict of genetic background from specimen.

forward to next link

 

© 2010, Laboratory of Systems Biology and Network Biology,

Institute of Information Science, Academic Sinica, TAIWAN.

All rights reserved.  Lasted updated 2010/05/25

user_defined unigene user_defined