AlleleID is a comprehensive primer and probe design software for real time PCR/microarrays. The software supports multiple real time PCR chemistries such as TaqMan, TaqMan MGB, molecular beacons, FRET, MLPA, Pamgene arrays and SYBR Green. AlleleID has multiple algorithms that follow the assay design guidelines of these chemistries.
AlleleID allows the users to input their nucleotide sequences by manually entering them or by downloading from NCBI Entrez. THe software also BLAST searches the sequence and interprets the results of these searches by avoiding the significant cross homologies.
AlleleID also does a template structure search and avoids regions that may fold upon themselves.
Users can design optimal TaqMan probes, TaqMan MGB probes, molecular beacons, SYBR Green primers, MLPA probes and Pamgene probes free of dimers, runs, repeats and other secondary structures.
The software screens the oligos (both primers and probes) for melting temperature requirements and user can specify the target and tolerance values. The oligos are never designed outside of these limits. Thus the stringency and flexibility is completely in users hands.
THe distinguishing feature of the software is its ability to design assays for detecting similarities and dissimilarities in a set of closely related sequences. The program supports multiple sequence alignments using ClustalW.
The users can perform an alignment in the program and can load an existing alignment file. Users may design assays (primers and probes) on either conserved regions for taxa detection or cross species amplification or for finding out a species from a mix.
The program designs multiple PCR primer and probes sets (assays) from which the user can choose the one he thinks might be most suitable.
The program can also evaluate oligos from published results or successful assays performed previoulsy. The program can also find suitable partnering oligos for primers and probes.
There is an option using which users can export the results of their designs in csv files. The primer probe design results can also be exported in the format of a report.
Here are some key features of "AlleleID":
· Real Time PCR Primer Design
· SYBR Green Primer Design
· TaqMan Probe Design
· Molecular Beacon Design
· FRET probe design
· Microarray Probe Design
· Database Support
· Input & Output Formats
· CPU: Pentium-IV 1.80 GHz
· RAM: 256 MB of available RAM
· Hard Disk Drive Space :500 MB of available hard disk
· Screen Resolution: 800 X 600
· Limited to the sample data provided.
- It accommodates the latest changes at the mFold and the NCBI BLAST server including support for the latest genomic database.