15-11-2006

CLC bio New Hardware Accelerator

CLCbio have created the ‘CUBE’. A hardware unit which runs Smith Waterman up to 125 times faster than a 3 GHz desktop computer.

Using the Cube instead of BLAST, improves the quality of the data you're working with! read more..

Beacon Designer Features

Avoid Cross Homology: Designs primers avoiding regions of cross homology. Beacon Designer BLASTs your sequences, automatically interprets the results and then designs highly specific primer pairs.
Design primers: Designs primers optimized for SYBR® Green assays.
BLAST: Primers can be BLASTed against genomic databases available at NCBI. This helps verify the primer design and visualize primer specificity.
Template Secondary Structures: Folds templates using the MFold program. Beacon Designer then automatically avoids secondary structures in the template when designing primers and probes.
Algorithm: Calculates Primer Tm using nearest neighbor thermodynamic algorithm.
Primer rating: Ranks primers according to expected priming efficiency.
Comprehensive criteria: Screens primers for their thermodynamic properties, location and secondary structures.
Multiplex Primers: Avoids cross homologies with all other dimers to reduce primer dimer.
Pre-designed primers: Designs optimal beacons for use with preexisting primers.
SNP amplification: Designs primers to amplify SNP sites.

TaqMan® probes: Designs optimal TaqMan® probes free of dimers, repeats and runs to ensure signal fidelity.
Multiplex & Allele discrimination assays: Supports multiplexing for up to four sequences, avoids cross homologies with all probes and primers preventing competition in multiplex reactions. Designs wild and mutant TaqMan® probes as well.
Evaluate pre-designed TaqMan® assays: Pre-designed primer sets can be evaluated or primers for a pre-designed probe can be constructed. Similarly, a pre-designed TaqMan® probe can be evaluated or a probe can be designed for a pre-designed primer set. You can even import the primers designed in the SYBR® Green primer design mode.
Algorithm: Calculates Tm using nearest neighbor thermodynamic algorithm.
Graphical view: Displays a graphical view of probe secondary structures.
Ranking: Only the best TaqMan® probes are designed for each template, using statistical optimization techniques.

Beacon Designer designs LNA™ or Locked Nucleic Acid™ substituted TaqMan® probes to improve real-time PCR assay success.
Design LNA™ spiked probes: Simply specify the numbers of LNA™ bases, their placement, and the length of the LNA™ free region on each end to design LNA™ spiked TaqMan® probes.

Predict CpG islands: Beacon Designer predicts the CpG islands in accordance with Gardiner-Garden and Frommer guidelines. You can also manually specify CpG islands in a sequence. The CpG islands are displayed in green and the GC rich region in red.
TaqMan® probes & Methyl Sensitive PCR primer design: The MethyLight Assay involves treatment of genomic DNA with sodium bisulphite followed by an alkaline treatment. Beacon Designer displays the corresponding bisulphite treated strand when the genomic sequence is provided. The methyl sensitive PCR primers and TaqMan® probes are designed for the CpG island specified. These primers and TaqMan® probes are highly specific as they are designed by avoiding regions of significant cross homology identified by automatically interpreting BLAST search results. Template structures, identified by connecting to the mFold server, are also avoided during the design.

Tm adjustment: Automatically selects a stem of appropriate length for optimal beacon Tm.
Optimal beacons: Designs beacons free of dimers, repeats, and runs for increased signal strength.
Multiplex beacons & primers: Checks molecular beacons for cross homologies with all primers preventing competition in multiplex reactions.
Allele discrimination: Designs molecular beacons for detection of both wild and mutant alleles.
Tm calculation: Highly accurate hairpin Tm calculation by connecting to the Mfold server.
Evaluate pre-designed molecular beacon assays: Pre-designed primer sets can be evaluated or primers for a pre-designed probe can be constructed. Similarly, a pre-designed beacon can be evaluated or a beacon can be designed for a pre-designed primer set. This facilitates using SYBR® Green primers for beacon assays.
Lightning fast: Processes an average cDNA sequence in under a second.
Graphical view: Displays designed beacon graphically along with its properties.

NASBA® assays: Short for Nucleic Acid Sequence Based Amplification, is gaining acceptance as an isothermal amplification process. It amplifies mRNA in double-stranded DNA without temperature cycling. Beacon Designer can design molecular beacon probes for NASBA® assays for single template, multiplex or alleleic discrimination.
Evaluate pre-designed primers and probes for NASBA® assays: While evaluating primers, Beacon Designer automatically adds a purine tag to P1 primer sequence when necessary.

Optimal FRET probes: Designs optimal FRET probes free of dimers, repeats and runs to ensure signal fidelity.
Allele discrimination: Designs FRET probes for detection of both wild and mutant alleles.
Evaluate pre-designed FRET assays: Pre-designed primer sets can be evaluated or primers for a pre-designed probe can be constructed. You can even import the primers designed in the SYBR® Green primer design mode.
Graphical view: Displays designed FRET probe graphically along with its properties.

BLAST search: Performs BLAST search on a selected sequence, primers and amplicon.
BLAST result views: Significant BLAST results are available locally for instant viewing.

Projects: Allows creation of multiple projects. A large amount of data can be easily organized and managed by creating a separate project for each experiment.
Built-in Database: Maintains a local database for sequence information and search results.
Data Export: Exports data in tab delimited format for easy loading into spreadsheets and databases.

Web Entrez: Quickly retrieves batches of sequences from Entrez using accession numbers.
BLAST search: BLAST search of any loaded sequence can be performed with a click of a button.

Generate Report: You will now be able to create an attractively formatted report for the assays you designed. It should be helpful in record keeping and for sharing information with colleagues. The report helps visualize the positions of the primers and probes on the sequence, includes a list of the alternate primers and probes, displays primers, probe, amplicon and sequence properties and the design parameters used.
Sequence details view: Comprehensive information of all sequences in a project is available locally using the built-in database and the sequence details can be viewed using your browser from within the program.
Sequence Visualization: Graphically displays the primers and probes on the sequence.
Input formats: Supports sequences in standard GenBank and FASTA format. Using the multiple retrieval facility, sequences can be loaded from local drives.
SNP loading: Easily loads thousands of SNPs from the variation descriptors in standard GenBank variation files.
View output in spreadsheet: Results can be viewed and manipulated in any spreadsheet like MS Excel, Lotus 123 or StarOffice spreadsheet.