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!

Author Archives: Chris

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 […]

Posted in Tips | Tagged , , | Leave a comment

How to retrieve BLAST hits from the Aligned Sequences result tab

After a BLAST search, you can retrieve matching sequences from the Description List results tab. What you may not know is that you can do a similar thing from the Aligned Sequences result tab. One advantage of this approach is that (as in the example above) sometimes there are multiple accession numbers for a hit. […]

Posted in Techniques, Tips | Tagged , | Leave a comment

Displaying CDS features as translations in the Map tab.

MacVector uses CDS features extensively in many areas. If you know the coding region, then it’s very useful to have that annotated to your sequence. For example you can display a CDS feature as its translation directly under the sequence in the Editor tab. You can also display the translation of a feature in the […]

Posted in Tips | Tagged | Leave a comment

Screening for CRISPR Indels using Align To Reference

MacVector’s Analyze | Align To Reference… tool is ideal for screening reads for the short insertions, deletions or substitutions resulting from CRISPR experiments. Simply open your reference sequence, choose Analyze | Align To Reference…, click on the Add Seqs toolbar button to add reads from different clones/experiments, then click on Align to align the reads […]

Posted in Tips | Tagged , | Leave a comment

How to align DNA sequences based on their amino acid translations

A new tool in MacVector 15 allows you to align DNA sequences based on their amino acid translated sequence. For most alignments in MacVector you will use the Multiple Sequence Alignment tool. This allows you to align DNA or protein sequences using either Muscle, Clustalw or T-Coffee. MacVector 15 now allows you to align DNA […]

Posted in Tips | Tagged , | Leave a comment

Functional domain analysis of protein sequences using InterProScan

There’s a new tool in MacVector 15 that allows you to do functional domain analysis on your protein sequence using the InterProScan service. InterPro contains multiple databases of protein families, domains and motifs and InterProScan will submit a protein sequence to a search of these databases. It will also do extra analysis such as transmembrane […]

Posted in Techniques, Tips | Tagged , | Leave a comment

Create your own Primer Database.nsub from an Excel spreadsheet

Wouldn’t it be great if there was an easy way of converting that huge primer collection you have into a format that MacVector can use? Well, luckily there is! There is a utility called “Primer Converter” that you can download from our website. To use the utility you first need to get your primers into […]

Posted in Techniques, Tips | Tagged , , | Leave a comment

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

It’s easy to keep track of all your primers using a MacVector subsequence (.nsub) file. We even ship MacVector with a starter file called “Primer Database.nsub” that you can find in the /Applications/MacVector/Subsequences/ folder. If you choose Analyze | Primer Database Search… and use this default file to search pUC19, you’ll find many of the […]

Posted in Tips | Tagged , , , | Leave a comment

Batch auto annotation of blank sequences with MacVector and AppleScript

Over the past few releases we’ve been making more MacVector tools to be scriptable with AppleScript. The latest is Auto Annotation. Auto Annotation is a great tool for curating your sequences. For example if you receive a unannotated sequence then you can scan it against other sequences to find. Blasting an unknown sequence, fetching the […]

Posted in Uncategorized | Tagged , | Leave a comment

MacVector For Windows update

It’s been some time since since the last update about MacVector for Windows, although development has certainly not been quiet. Here’s some screenshots. Graphical Map Sequence Editor Automatic Restriction Enzyme and ORF Analysis Primer Design Cloning Clipboard Tweet

Posted in Releases | Tagged | 1 Response