Category: Tips
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Simple Assembly of Sanger Sequencing Files with MacVector Assembler
With MacVector Assembler, assembling ABI Sanger Sequencing files is simple, fast and accurate. MacVector uses the popular phred/phrap/cross_match set of tools from the University of Washington. To improve accuracy, and to help resolve repeats, these tools use “quality scores” (popularly known as “phred scores”), giving them an advantage over many other methods. To assemble two…
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Assembling sequencing data with MacVector and Assembler
MacVector has a software plugin called Assembler that integrates directly into the DNA sequence analysis toolkit and provides DNA sequence assembly functionality. Dealing with sequencing reads has never been easier. MacVector includes no less than five different assemblers just a few mouse clicks away from your sequencing reads. Phrap assembles Sanger sequencing reads or existing…
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MacVector video tutorials on You Tube
There are short video tips on using MacVector on our blog and our YouTube channel. Each one is less than 2 minutes and generally shorter than that! There will be a new screencast every few weeks, so please subscribe to our YouTube channel so you don’t miss any! The latest screencasts include quickly annotating a…
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Viewing external database entries for features in a sequence.
Sequences, or regions of sequences, can be linked to external databases. For example an entire sequence entry or for when annotation tools are used to annotate proteins with domain or motif information (for example InterProScan). Very useful for when you want to view more detailed or updated information. Within the Genbank specification, which MacVector extensively uses,…
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Use the Replica Button For Synchronized Views
Most primary MacVector windows (Nucleic Acid Sequence, Protein Sequence, Multiple Sequence Alignment, Align To Reference, Contig Assembly etc.) have a Replica toolbar button. If you click that button, a second window will open, potentially set to a different tab. The key to this functionality is that the two windows are linked – any selections you…
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How to Identify Bacterial Promoters Using MacVector
MacVector’s Subsequence tool is a very flexible search function that can be used for a variety of tasks. MacVector itself has a built-in variant of the function for maintaining and search primer databases (Analyze | Primer Database Search…). Each entry in the file MacVector uses as a source of subsequence data can have up to…
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Import Multi-Sequence Genbank Files into an Assembly Project for easy access to Features
There are many genomes in the Genbank database that cannot be downloaded as single annotated sequences. These might be large multi-chromosome eukaryotic genomes, but, increasingly, partially sequenced bacterial chromosomes where the major contigs have been annotated using the NCBI annotation pipeline. Typically, when you encounter these, there are options to download annotated versions of these…
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Opening multiple sequences as alignments or individual sequences
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.…
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Restoring file associations when MacVector no longer opens your sequences
Macs are pretty good at choosing the right application to open a document. For example when you double click on a .nucl document then it will open in MacVector. However, sometimes this file association breaks. Applications should coexist peacefully on a Mac, but sometimes a misbehaving app will corrupt these file associations and you will…
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Searching and downloading sequences from Entrez
MacVector has integrated connectivity to the NCBI BLAST and Entrez databases. You can directly search Entrez for DNA or Protein sequences based on features, authors, keywords etc and directly download them into MacVector, complete with all features and annotations.