MacVector’s Analyze | Create Dot Plot function can be used to compare entire genomes very quickly to get both an overall view of similarity (large inversions and duplications) while providing the ability to “drill down” to the residue level to see individual SNPs. One of the keys to ensuring the calculations complete in a reasonable […]
MacVector 18.2 Overview We are very pleased to announce that MacVector 18.2 is available to download. MacVector 18.2 is a Universal Binary that runs natively on both Apple Silicon and Intel Macs. It is fully supported on macOS Sierra (10.12) to macOS Monterey (12). New features: Align to Reference Enhancements The Align to Reference alignment algorithm […]
In recent years there has been an explosion of whole-genome sequencing projects. One common question coming out of this has been to ask: “Exactly what are the genetic differences between my sequenced organism and another related strain?” MacVector to the rescue! MacVector’s Compare Genomes By Feature… tool lets you see the differences between two annotated […]
Many sequence formats contain multiple concatenated sequence entries. For example FASTA and Genbank are two formats capable of storing multiple individual sequences. By default MacVector will treat such sequences as alignments and open them in the Multiple Sequence Alignment editor. Most users who want to open such a file do want to see an alignment. […]
Many sequence formats contain multiple concatenated sequence entries. For example FASTA and Genbank are two formats capable of storing multiple individual sequences. By default MacVector will treat such sequences as alignments and open them in the Multiple Sequence Alignment editor. Most users who want to open such a file do want to see an alignment. […]
Here’s what MacVector can do for your lab. Comparing sequences Whatever type of alignment your sequence needs, there’s a tool in MacVector. CRISPR Indel Analysis: Identify insertions and deletions following CRISPR editing of a target. Sequence assembly of NGS data against a reference genome or compare your sequencing against your new construct. Translated Multiple Sequence […]
If you are screening a set of clones for the presence of changes after a CRISPR experiment, then the MacVector Analyze | Align To Reference functionality is the approach to use. However, you may find that the default parameters are not ideal for this type of analysis – they are tuned for simple sequence confirmation […]
The Database | Align To Folder function is an extremely useful tool to help you find matching sequences on your own local file system. It is essentially a BLAST search of your own private sequence collection – a little slower, but more sensitive. You can use it to easily open all of the sequences you […]
The classic algorithm for aligning multiple protein sequences is ClustalW. Normally, it does a great job of aligning related DNA and Protein sequences and can handle thousands of sequences if required. However, one place where it struggles is if you are aligning non-overlapping segments of DNA or Protein against a parental full-length sequence. The reason […]
Sometimes it is useful to sort, or cluster, an alignment according to the similarity/identity of its sequences. With such a sorted alignment you are able to more easily visualise closely related sequences as they will be together in an alignment with more distantly related sequences being much further apart. If you want to quickly cluster […]