Thanks for those who have participated in our latest Survey Contest on 9/15/09.
Here is the list of our randomly selected winners for the $25 Amazon.com Gift Certificate:
Winners will receive the prize via e-mail soon.
Congratulations!!
-The MiraiBio Team
You have spoken and we have listened. For a while now, we have seen requests for a primer tool that is capable is designing primers that are specific to the input PCR template. NCBI has just recently developed such a tool, Primer-Blast, and we have just finished incorporating it into DNASIS SmartNote!
DNASIS SmartNote users now have the ability to select an organism by name or taxonomy id when utilizing the Primer-Blast tool. The tool will design the primers and blast them against the specified genome. The blast results are then analyzed to filter out primer pairs that can cause amplification of targets other than the input template ensuring that the primers you get will be specific.
DNASIS SmartNote users can then easily extract these primer sequences for downstream analyses such as the IDT Oligo Analyzer which includes a Homo-Dimer Analysis as well as some specifications of the oligo which include molecular weight, extinction coefficient, and much more.
For those that are new to DNASIS SmartNote, all your results and sequences are automatically saved for you in your electronic bioinformatics lab notebook so that you can access the information whenever you like and where ever you have an internet connection.
Here is a preview of one of the pages from my SmartNote notebook showing the Primer-Blast and IDT Oligo Analyzer results utilizing the share feature.
Here are some sample screenshots of the Primer-Blast results from the DNASIS SmartNote application:
Primer-Blast results from DNASIS SmartNote web application
IDT Oligo Analyzer - Homo-Dimer Results from DNASIS SmartNote web application
Get your FREE DNASIS SmartNote account and take it for a test drive!
We are now making it even easier to begin analyses after importing your sequences. After a successful import, you will be asked what you would like to do with your sequences. If you choose Analyze, your sequences will automatically be added to your sequence cart and you will be taken to the tools list where you can select which analysis you would like to perform.
The tools list page has also been updated so that it is more user-friendly. We now have a Quick Launch feature which will automatically launch the tool of interest by using the default parameters. If you would like to change the parameters for a given tool, simply click on the tool name and you will be taken to the default tool page where you can adjust parameters and launch the tool.
These are just a few of the features that we have implemented for a smarter more intuitive interface for any user. If you are interested in seeing these features in action, sign up or login to DNASIS SmartNote.
An online social community for nearly every niche exists on the internet. MiraiBio understands this so now, there is one for the Luminex Community, MasterPlex Community, and DNASIS Community.
In addition to the online community members, MiraiBio’s own employees will be browsing around as well joining in on all the conversations. So whether you were just curious about something or need help troubleshooting, feel free to drop by and start a converation!
DNASIS SmartNote is a web application that is capable of doing what a stand-alone desktop software does BUT inside a browser. With this capability comes some requirements needed to power the web application. Here is a list of some requirements as well as some recommendations to optimize your DNASIS SmartNote experience:
Many of the FlexMAP (now called xTAG) microsphere users relied on the TagIT software to help choose which microsphere sets to use in genetic detection assays run on the xMAP platform. When the TagIT software was removed these users no longer had a reliable way to design their assays. Well the good news is that TagIT is back!
Hitachi Software recently released a free software tool to automate the design of SNP genotyping assays using Allele Specific Primer Extension (ASPE) on the xMAP platform. The ASPE approach utilizes Luminex Corporation’s xTAG (formerly FlexMAP) microspheres which are pre-coupled to oligonucleotide sequences (anti-tags) that are optimized to be an isothermal set and to have minimum cross-reactivity. The detection probes have the tag sequence synthesized on the 5′ end. The use of the pre-coupled xTAG microspheres simplifies the assay greatly.
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.
NCBI BLAST, the Basic Local Alignment Search Tool (BLAST) is a suite of programs designed to search all available sequence databases for similarities between a protein or DNA query and known sequences. BLAST allows quick matching of near and distant sequence relationships, providing scores that allow the user to distinguish real matches from background hits with a high degree of statistical accuracy.
Focusing on local alignments, BLAST uses a heuristic algorithm to detect relationships between sequences that may only share isolated regions of similarity. BLAST results take sequence length and the nucleotide/peptide compositions of the query into account when assigning alignment scores. For sequences shorter than 200 residues, an effective length is used to compensate for “edge effects”. Sequence alignment scores are reported by BLAST programs as E-values that reflect the strength of alignment between a given sequence in the database and a query. E-values are reported instead of the traditional P-value, to improve resolution between low scoring alignments, but for closely related sequences (P < 0.01), these values are nearly equal.
For more detailed information on how BLAST scores are calculated, visit:
http://www.ncbi.nlm.nih.gov/BLAST/tutorial/Altschul-1.html
For most first-time users of BLAST, choosing the right sub-program may be difficult. BLAST offers a variety of search tools for different types of queries. In general, the best choice of program depends upon the sequence length, the database being searched, and the information requested in the search.
Nucleotide BLAST is a collection of programs allowing users to compare a query sequence against other nucleotides in the database. BLAST accepts sequences in a variety of formats, including FASTA, GenBank, and Accession/GI numbers, and compares these with the NCBI databases. MEGABLAST is a concatenating algorithm for quickly aligning sequences longer than 28 residues. For shorter sequences, such as primers, standard nucleotide-nucleotide BLAST offers automatic parameter settings suited to these queries.
Protein BLAST is a collection of programs used to find protein sequences similar to a query. These programs accept sequences in the same file formats as Nucleotide BLAST. PSI-BLAST is a position specific, iterating algorithm that searches sequences from each round as the basis for scoring sequences searched in the next round. It distinguishes between highly and weakly conserved positions in the sequence, resulting in increased sensitivity with each iteration. PSI BLAST also offers the option of including regular expression patterns in the search, allowing users to identify sequences that include a pattern and are homologous to the query protein sequence. As with Nucleotide BLAST, Protein BLAST includes automatic parameter settings for shorter sequences.
Translating BLAST operates in a similar fashion to both the nucleotide and protein search routines. BLASTX translates nucleotide sequences into protein sequences in each of the 6 reading frames, prior to comparing the query to the protein databases. TBLASTN compares a protein sequence query against a database of nucleotide sequences previously translated in each of the 6 reading frames.
Users can refer to the NCBI BLAST program selection guide for more information:
http://www.ncbi.nlm.nih.gov/blast/producttable.shtml.
Users can access BLAST tools directly through the web, or through a variety of software applications, such as MiraiBio’s DNASIS SmartNote, which helps users find and organize sequences, and automatically submit them to the BLAST programs. DNASIS SmartNote has the additional ability to BLAST multiple sequences “in batch” without tediously copying/pasting each sequence and waiting for each result to come back.
To learn more about DNASIS SmartNote, visit http://smartnote.miraibio.com.
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”
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
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.
