Tag: weeklytip

  • Calculating the optimal PCR annealing temperature

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    Chris
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    MacVector has several tools to help with primer design and testing. The Analyze | Primer Design/Test (Pairs) function uses the popular Primer3 algorithm to find suitable pairs of primers to amplify specified segments of DNA. You can also enter pairs of pre-designed primers and test their suitability for use in PCR. In both cases, the…

  • How to copy a specific short amino acid translation of a sequence

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    Chris
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    There can be times when you are messing about with open reading frames, inserting residues to change frames to try to get the perfect CDS fusion. The MacVector single sequence Editor will show those (click and hold on the “Display” toolbar button) but if you select and copy, only the DNA sequence (with any overlapping…

  • Optimizing Reverse Translations

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    Chris
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    The Analyze | Reverse Translation menu option lets you create a DNA sequence from a Protein sequence, reverse translated using a specific Genetic Code (by default, the Universal Genetic Code). The default option creates a DNA sequence with N’s and other ambiguities reflecting the degeneracy of the genetic code. This is great if you want…

  • Use Database | Auto-Annotate Sequence to annotate prokaryotic genomes

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    Chris
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    The continuing advances in Next Generation Sequencing have made it relatively low cost to sequence prokaryotic genomes. Many scientists are embarking on large projects to sequence multiple related genomes. These might be clinical isolates of the same species exhibiting different pathogenetic properties, environmental isolates from different sites, or a study over time of the changes…

  • Which DNA Matrix to use in Align To Folder?

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    Chris
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    The Database | Align To Folder function is a very useful tool to find and retrieve similar sequences from folders on your computer or on other local machines. Think of it as your own personal BLAST service. It can not only search individual sequences in any format MacVector can read (MacVector, Genbank, EMBL, ABI etc)…

  • Gap closing and genome finishing tools in Align to Reference and Assembler.

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    Chris
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    Automated algorithms can only take you so far with genome assembly. The final steps involved in finishing a genome always need manual intervention. MacVector’s various assembly editors have many tools for helping finish genome sequencing projects. For example, closing gaps, extending reference sequences and even automatically circularizing contigs. If you select reads, then right click…

  • Use a right-click in the Editor tab to see if your contig can be circularized

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    Chris
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    MacVector incorporates no less than THREE different de novo assemblers, phrap, velvet and SPAdes. While all are great assemblers, with each having their own specific advantages, none of them will generate a circular sequence from input reads. However, MacVector also includes a tool to help you with this. If you are assembling reads representing plasmid…

  • Import Multi-Sequence Genbank Files into an Assembly Project for easy access to Features

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    Chris
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    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…

  • Opening Genbank or FASTA files with multiple sequences as individual sequences

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    Chris
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    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.…

  • Optimizing Align To Folder Parameters for use with NGS Data

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    Chris
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    You can use the Database | Align To Folder function to scan large fasta or fastq files containing NGS data to find and retrieve just those reads that match a specific target sequence. The search is aware of paired-end reads, so when you retrieve hits, both reads of a pair will be saved into a…