We’ve talked in previous tips about annotating open reading frames as CDS features. However, what if your sequence has no annotated ORF? MacVector’s ANALYZE | OPEN READING FRAMES… tool will help you find any quickly. However, if you are new to this tool there are a few options that may prove initially confusing. These options […]
Although QuickTest Primer is intended for designing primers, the interface is very flexible. If your sequence is not too long, you can use the Quickest Primer interface to scroll through a sequence and visually look for hairpins appearing in the hairpin pane. The easiest way to do this is to select the first ~100 nt […]
It’s very quick to download the latest version of a sequence if you know its accession number. When you start working with a new sequence, it’s the best place to start. Go to DATABASE > ENTREZ Enter the accession number of your favorite sequence Click SEARCH Double click on the result to open up your […]
When you run a Blast search, as well as a list of hits, you will get a list of alignments between your query sequence and each hit. As with most other text alignments in MacVector, identical matches are by default represented by a vertical line (a score greater than 1) and mismatches (whether similar or […]
The MacVector Assembler module lets you create projects, populate them with Sanger Sequencing or NGS data files (or any sequences in a format that MacVector can read) and then assemble them using the popular phrap and/or Velvet assemblers. Typically, the result will be a collection of contigs that you might want to use in additional […]
The Database | Align To Folder… function is essentially your own personal BLAST search of sequences on your computer, but with the advantage that you can scan fasta/fastq containing millions of entries and retrieve matching Reads into a new file. MacVector 14.5 added an enhancement where you can search paired-end read files and retrieve both […]
After a BLAST search, you can retrieve matching sequences from the Description List results tab. What you may not know is that you can do a similar thing from the Aligned Sequences result tab. One advantage of this approach is that (as in the example above) sometimes there are multiple accession numbers for a hit. […]
MacVector uses CDS features extensively in many areas. If you know the coding region, then it’s very useful to have that annotated to your sequence. For example you can display a CDS feature as its translation directly under the sequence in the Editor tab. You can also display the translation of a feature in the […]
MacVector’s Analyze | Align To Reference… tool is ideal for screening reads for the short insertions, deletions or substitutions resulting from CRISPR experiments. Simply open your reference sequence, choose Analyze | Align To Reference…, click on the Add Seqs toolbar button to add reads from different clones/experiments, then click on Align to align the reads […]
A new tool in MacVector 15 allows you to align DNA sequences based on their amino acid translated sequence. For most alignments in MacVector you will use the Multiple Sequence Alignment tool. This allows you to align DNA or protein sequences using either Muscle, Clustalw or T-Coffee. MacVector 15 now allows you to align DNA […]