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: weeklytip

Subscribe to Weekly Tips

A few tips on working with digested fragments in the Cloning Clipboard

Annotating the sequence in the Editor tab

Calculating the melting temperature of PCR primers

Calculating the PCR annealing temperature for a pair of primers

Changing the sequence alignment match and mismatch characters

Clearing the history in the Primer and Find dialogs

Controlling the realism of Agarose Gels

Create constructs using the Cloning Clipboard

Create your own Primer Database.nsub from an Excel spreadsheet

Creating a custom set of restriction enzymes containing just the enzymes in your freezer drawer.

Creating cloning construction flowcharts in third party applications

Designing and documenting cloning strategies

Displaying CDS features as translations in the Map tab.

Displaying CDS features as translations in the Map tab.

Displaying features in the Editor tab

Download the latest published version of your favorite sequence with its accession number

Downloading BLAST Hits from the NCBI

Downloading BLAST Hits from the NCBI direct to your desktop

Drag and drop to quickly annotate ORFs

Editing the appearance of your sequence maps

Functional domain analysis of protein sequences using InterProScan

Generating a primer report to send to your Oligo Synthesis service

Highlighting sequence using color and lower case in the Editor tab

How to align DNA sequences based on their amino acid translations

How to automatically annotate bare sequences

How to change the circular origin of a sequence

How to change the default appearance of RE sites

How to display and manipulate segmented Features

How to display translations in the sequence editor

How to find and open all the sequences on your computer containing a specific gene.

How to identify methylation blocked Restriction Sites

How to import annotated GenBank sequences via copy and paste

How to increase the number of graphics levels to stop features overlapping.

How to increase the number of graphics levels to stop features overlapping.

How to make feature arrows point in the other direction

How to remove gaps from a sequence

How to reset the numbering after pasting a DNA fragment

How to reset the sequence numbering when working with a subsection from a larger sequence

How to reset the zoom level when you Drag Zoom into your sequence.

How to retrieve BLAST hits from the Aligned Sequences result tab

How to select all identical restriction enzyme sites

How to toggle between 1 and 3 letter amino acid codes

How to use Codon Preference plots

Importing sequences/features from websites such as ENSEMBL or UCSC’s Genome Browser

Keep up to date with MacVector auxiliary files

Know Your Alignments

Opening matching sequences from an Align To Folder search

Optimizing the Reverse Translation function

Organising your sequences using Smart Folders

Print Agarose Gel images with black bands on a white background

Quick shortcuts to zoom in and out in the Single Sequence Map tab

Quickly checking a small sequencing project

Quickly design a pair of primers to amplify a feature

Removing a restriction site from a plasmid with the Cloning Clipboard

Restriction enzyme analysis in MacVector and REBASE

Restriction enzyme sites and tooltips

Restriction enzyme sites in cloning vectors show compatible ends with fragments in the Cloning Clipboard

Save trace files as images

Screening for CRISPR Indels using Align To Reference

Search fastq files and retrieve matching reads into paired fastq files

Selecting sequence residues in the Map tab

Smart Folders and MacVector

Subscribe to Weekly Tips

Tear-off Result Window Tabs

Tear-off Result Window Tabs: make viewing results easier.

Test PCR Primer Pairs using the Primer Design (Primer3) Interface

Testing pairs of PCR primer

Testing pairs of primers

The easiest way to get graphics out of MacVector

The Importance of Topology

The simplest way to export high quality graphics from the Map tab

Troubleshooting problems with MacVector

Troubleshooting problems with MacVector

Tweak your DNA Matrix for better Align To Folder searches with primers

Use Analyze -> Align To Reference to align ABI trace files

Use Analyze->Primer Database Search to scan sequences for primer binding sites

Use dot plots to quickly confirm similarity between two sequences

Use File -> New From Clipboard to create new sequence documents

Use the [option] key to paste, or ligate, in the opposite orientation

Using BLAST to automatically annotate a sequence

Using the Primer Database to store your lab’s collection of primers

Using the Primer Database to store your lab’s collection of primers

View sequences at the residue level in the Map tab

Viewing external database entries for features in a sequence.

Viewing raw chromatogram data from .ab1 files

Visualizing ORF analysis results in the MAP tab

Working with digested fragments in the Cloning Clipboard

You can automatically use the Free version of MacVector if your serial number is in use