Category Archives: Algorithms

MacVectorTip: “Nudge” Reads for Better Reference Alignments

The MacVector alignment algorithms are usually pretty good at finding the optimum alignments of reads against a reference sequence. But, very occasionally, they may get confused by repeats or other anomalies in the sequences. Or perhaps you have made after-the-alignment edits: for example, in the Align to Reference Editor, you can insert residues by holding […]

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How Assembler uses quality scores to create assemblies

A common problem with all types of sequence assembly is distinguishing between sequencing errors and true genomic variations. Quality scores are one way to help the algorithm identify if a variation is of high quality and therefore likely to be a SNP or a sequencing error. For Assembler trace files can be basecalled with Phred, […]

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Assembler: Using the coverage map of the Reference Contig editor to analyze your assembly

There are two main steps to creating a reference assembly. Mapping your reads against your reference sequence and then analysing the alignment for variations. Knowing the depth of reads, or coverage, of an alignment is important for both of these stages. A low average depth of coverage means that you have less confidence in the […]

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MacVector 12.5: Creating alignments with T-Coffee and Muscle

With MacVector 12.5 we’ve added additional multiple sequence alignment (MSA) algorithms. Muscle and T-coffee have been added to the Multiple Sequence Alignment editor complementing the existing ClustalW algorithm. We’ve wanted both of these for a while now and judging from the results of last year’s survey so have many users. Both T-Coffee and Muscle are […]

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Changes to isoelectric point calculation in MacVector

We have a policy of constant improvement in all areas of MacVector, even with algorithms and analyses that have been the same for many years. Recently we changed the way that the isoelectric point of a protein was calculated. The previous version of the algorithm was accurate for short proteins, however for longer amino acid […]

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Short read improvements to MacVector 11.1

The ability to produce de novo assemblies of short read data was introduced into MacVector & Assembler 11 and we’ve enhanced this in MacVector 11.1. Now Assembler stores and visualises metadata on the type of short read you have and also stores and deals with the quality data stored in a better way. Mixing your […]

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Auto Annotation in MacVector 11

Have you ever got that plasmid back from the sequencing facility as a bare sequence with no annotations? Or downloaded that vector from from the vendors site to find its only available in a fasta format with no features? Or maybe your collaborators send you poorly annotated sequences. Maybe your lab-mate uses MacVector but insists […]

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Topology of a sequence and interface changes

With each new release of MacVector we have always strived to be the easiest to use sequence analysis application. We have made some fairly radical changes to the interface over the last few years, and inevitably there are some changes that you know will confuse long time users but are needed to make the interface […]

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Alignments in MacVector

Update 19 August 2013: We’ve added support for Muscle and T-Coffee to the MSA editor We get a lot of comments and questions from users on the various alignment functions in MacVector. They say there’s more than one way to skin a cat (not that I’ve done that – I have skinned a catfish, but […]

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