1. DNASIS SmartNote now shows a graphical view of any sequence annotations included in files imported from Entrez. To see it, click the “Details” link next to the sequence in the “My Sequences” view. Here’s what it looks like:
2. The xTAG Tool now lets you exclude certain bead regions. In addition, its results now also include tag and anti-tag sequences.
We have 3 improvements to report for DNASIS SmartNote this week, all having to do with more efficient sequence importing and exporting:
1. Accession number recognition - DNASIS SmartNote now recognizes accession numbers in sequences you import (or will ask you to enter one if you paste in a raw sequence). This gives you better control over the naming of your sequences, so you can keep better track of which results belong to which sequence.
2. Import multiple sequences at once - If you’d like to import several sequences into DNASIS SmartNote and you know their accession numbers, you can now enter them all (separated by commas). To try it out, click on “Get Sequences” under DNASIS SmartNote’s “Sequences” tab, then select “Search for sequences from NCBI Entrez” or “Search for SNPs from NCBI DB”
3. Export raw results from xTAG Software tool - For those who are using DNASIS SmartNote’s new tools for designing tagged, gene-specific oligos (GSO) for their Luminex assays using Universal Array beads, the xTAG tool can now export results as comma-separated values (CSV), so you can transfer the data to Microsoft Excel or other spreadsheet programs. The output fields are: “Sequence Name”, “Bead Region” and “Oligo Sequence”
From MiraiBio’s blog:
Hitachi Software’s MiraiBio Group has recently launched 2 new software tools in the DNASIS SmartNote web application: the Allele Specific Primer Extension (ASPE) Assay Design tool and the xTAG Software (formerly TagIT) tool. These tools are important time savers for those who are interested in multiplexing their SNP or genotyping assays on the Luminex xMAP (also sold by Bio-Rad as the Bio-Plex) platform.
The ASPE Assay Design tool designs probes and primers by optimizing melting temperatures and screening for cross reactivity among the probe and primer sets. All you have to do is to provide the tool with your sequences, SNP position, and allele variants (if you have the SNP rs accession number this information will automatically be populated ). You will get a comprehensive report on the amplification primer pairs that are recommended along with the tagged allele specific primers and the corresponding MicroPlex xTAG Microspheres (formerly FlexMAP beads) to use in your assay. You will even be able to purchase the Microspheres directly from Hitachi Software! It doesn’t get any easier than this.
If you have already designed your allele specific primers, then you have the option of using the xTAG Software tool to select the right MicroPlex xTAG Microspheres to use in your assay.
DNASIS SmartNote is a free web application that is an in silico lab notebook for molecular biologists. Use it to:
• Analyze sequences with dozens of tools
• Access and edit your notebook from anywhere
• Share sequences and results with friends
• Publish results to a blog