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.

Option 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.

Option 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.

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

Option 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.

 

Detail for each column:

We provide more information for each probe in following files.

Here are some examples for each item

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

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