The newly released version of DNASIS MAX has several new features:
Visit the DNASIS MAX v3.0 product page for more information or Download the 14-day Free Trial.
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!
DNASIS MAX has the ability to search for homologous sequences to your sequence with BLAST (Basic Local Alignment Search Tool). BLAST finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families.
The following procedure guides you through utilizing BLAST against NCBI’s sequence databases.
DNASIS MAX has the ability to search for homologous sequences to your sequence with Blast which is
useful in judging if the sequence is novel or even add annotations from known gene information. The following procedure guides you through utilizing Blast against an internal sequence database.
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.
MiraiBio has gone online with software. We are pleased to introduce a revolutionary way to store and analyze your sequences and share them with colleagues.
What can SmartNote offer to you?
1. A job queuing system was implemented – You no longer need to wait for compute-intensive results (e.g. BLAST searches on multiple sequences) to come back. Just submit a job and continue working. When the results are in, you’ll be notified.
2. You can now add comments to tools and read other users’ comments. See what your colleagues have to say about which tools are best for a given task, or if there’s any tips and tricks to get the most value from a tool.
3. Auto-scrolling to results has been fixed – When you click on a result in the left pane, the right pane will automatically scroll to the corresponding position on the page so you can instantly access any result.
4. More help features to guide new users – You’ll notice several new icons to help you use SmartNote’s features.
5. Other cool additions such as the new animated progress icon for the sequence manager window.
6. Many bug fixes – everything just works more smoothly.
Remember to tell us what you think about DNASIS SmartNote and what new features you’d like to see. We’ve been making changes weekly, so as long as your request is reasonable, we’ll most likely be able to add it.
