Interface of UPS

Starting from an intuitive web interface, users can submit single or multiple sequences in fasta format. Four options can be conducted for probe design in 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.

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.

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 allow users to upload a set of sequences or genomes in fasta format as the reference genetic background for probe design.

 

   
Output of UPS

Detail for each column:

Sequence_ID

:

Sequence Identifier derived from the original input sent by user

Rank

:

The order of best probes calculated by UPS

CG%

:

CG content inside the probe, the default range of CG% is between 35% and 75%.

Tm

:

Melting temperature, the constrain of Tm is between 70 and 90 XC.
To conduct the hybridization towards completion and speed hybridization, probes of RNA or DNA are usually hybridized 15-25XC below the actual Tm, and oligonucleotides are hybridized 5-10XC below the actual Tm.

Probe Sequence

:

The sequence for each selected probe

delta G

:

delta G is free energy calculated in thermodynamic approach related with the folding of each probe. The probe with delta G larger than zero means it is hard to form secondary structure and is more suitable for hybridization. 

   
Output for Download
We provide more information for each probe in following files.

download_file

Here are some examples for each item

1. Best probes in fasta format without cross-hybridization(Detail for In silico hybridization)

best_prob_wo_hyb

2. Best probes in fasta format

3. All probes in fasta format (Sequence_ID _ Rank)

4. All probes in CSV (with Tm, CG%, deltaG, Best_hit, Max_overlap, Identity )

Detail for each column:

Sequence_ID

:

Sequence Identifier derived from the original input sent by user

Rank

:

The order of best probes calculated by UPS

Initial position

:

The starting point on original sequence

CG%

:

CG content inside the probe

Tm

:

Melting temperature

CGinside

:

The CG content of each probe ranging between 35 and 75% will be marked with "Y". Otherwise, it will be marked with "N".

TMinside

:

The probe with Tm ranging between 70 and 90 XC will be marked with "Y". Otherwise, it will be marked with "N".

Probe Sequence

:

The sequence for each selected probe

Minimum freq

:

The frequency of K-mers combination

Hit_ID

:

Identifier for significant alignment sequence by BLASTn

Length of Hit sequence

:

The length of hit sequence

Identity

:

The identity between designed probe and hit sequence

Gaps

:

The gap between designed probe and hit sequence

Start position of query

:

Starting position of probe for alignment pair

End position of Query

:

Ending position of probe for alignment pair

Start position of hit

:

Starting position of hit sequence for alignment pair

End position of hit

:

Ending position of hit sequence for alignment pair

delta G

:

delta G is free energy calculated in thermodynamic approach related with the folding of each probe. The probe with delta G larger than zero means it is hard to form secondary structure and is more suitable for hybridization. 

QC

:

The value means "Quality Control". "Y" indicates this probe passed all the constrains, "N" shows this probe may fail to pass one or several constrains.

 

5. In silico hybridization check for each probe by BlastN

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© 2010, Laboratory of Systems Biology and Network Biology,

Institute of Information Science, Academic Sinica, TAIWAN.

All rights reserved.  Lasted updated 2010/05/25