General musings from the MacVector team about sequence analysis, molecular biology, the Mac in general and of course your favorite sequence analysis app for the Mac!

Tag Archives: assembler

Use File->Export in the Contig Editor to save selected reads

Last week we covered the fact that you can use File->Export to save sequences or alignments in different formats. Delving down deeper into this, some of the views will save different types of data based on what you select in the format menu. The best example of this is the Contig Editor. If you choose […]

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How to save contig consensus sequences from assembly projects

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 […]

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Search fastq files and retrieve matching reads into paired fastq files

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 […]

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Estimating insert length quickly for a read pair

Insert length is the length of the sequence in between a pair of reads. Sequencers are supplied DNA samples in fragments of a known length and each end is sequenced (generally in a 5′ to 3′ direction from both ends). For example if you have a fragment of 2Kbp and your reads had an average […]

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Know Your Alignments

We often get asked “how do I do an alignment” using MacVector? Well, the answer to that is always “it depends”, and it depends on what you want to learn about your sequence(s). Here’s a quick summary of the different types of alignments and what you would use them for: Multiple Sequence Alignment (File | […]

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Quickly checking a small sequencing project

For analyzing large sequencing datasets you need Assembler. However, many times you do not need a powerful tool but just a quick way to check some sequencing data. For example for checking small sequencing projects, such as a site directed mutagenesis, looking for SNPs in a PCR product, cloning a gene or checking your latest […]

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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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Quickly checking a small sequencing project

For analysing large sequencing datasets, whether de novo or mapping reads against a reference you need Assembler. However, many times you do not need a powerful tool but just a quick way to check some sequencing data. For example for checking small sequencing projects, such as a site directed mutagenesis, looking for SNPs in a […]

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101 things you (maybe) didn’t know about MacVector: #41 – Extracting raw data from chromatogram files

Have you ever wanted to know exactly what the total signal value is for individual peaks in a chromatogram file? Perhaps you are looking for mixtures of residues at a particular location and want to get some idea of the relative proportions? You can open .ab1 and .scf chromatogram files directly in MacVector and view […]

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101 things you (maybe) didn’t know about MacVector: #40 – Removing gaps from a DNA or protein sequence

There are often times when you end up with a sequence containing gaps, especially if you make extensive use of the Align To Reference, Contig Assembly or Multiple Sequence Alignment interfaces to generate consensus sequences. You can select and copy the consensus sequence, or even individual aligned reads, from the Align To Reference and Contig […]

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