-
How to Identify Bacterial Promoters Using MacVector
Read more: How to Identify Bacterial Promoters Using MacVectorMacVector’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…
-
Import Multi-Sequence Genbank Files into an Assembly Project for easy access to Features
Read more: Import Multi-Sequence Genbank Files into an Assembly Project for easy access to FeaturesThere 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 multiple sequences as alignments or individual sequences
Read more: Opening multiple sequences as alignments or individual sequencesMany 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.…
-
Restoring file associations when MacVector no longer opens your sequences
Read more: Restoring file associations when MacVector no longer opens your sequencesMacs 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…
-
What can MacVector do for me?
Read more: What can MacVector do for me?Here’s what MacVector can do for your lab. Comparing sequences Whatever type of alignment your sequence needs, there’s a tool in MacVector. CRISPR Indel Analysis: Identify insertions and deletions following CRISPR editing of a target. Sequence assembly of NGS data against a reference genome or compare your sequencing against your new construct. Translated Multiple Sequence…
-
Searching and downloading sequences from Entrez
Read more: Searching and downloading sequences from EntrezMacVector 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.
-
Eastern Great Lakes workshop tour in February
Read more: Eastern Great Lakes workshop tour in FebruaryThe MacVector team will be touring the Eastern Great Lakes for a series of workshops in February. We will be running workshops in Rochester NY, Buffalo NY, Ypsilanti MI, Cleveland OH, Wooster OH, Columbus OH and Cincinnati OH. Monday, Feb. 5th 10:00 – 12:00 University of Rochester, Rochester, NY 2:00 – 4:00 University at Buffalo,…
-
Using MacVector’s Auto Annotate tool to annotate blank sequences.
Read more: Using MacVector’s Auto Annotate tool to annotate blank sequences.Have you ever been sent a plain unannotated sequence, or downloaded a sequence from Entrez and been disappointed as it doesn’t have the carefully curated graphical appearance of your favorite genes? Auto annotation solves both of these common problems. The basic idea is that you can scan the sequence against a folder containing a…
-
Adding a primer to MacVector’s Primer Database.
Read more: Adding a primer to MacVector’s Primer Database.MacVector’s Primer Database tool makes it easy to store your lab’s regular primers. It allows you to save and retrieve primers from the Primer Database from the Primer3 and Quicktest Primer tools. You can also scan sequences for potential primer binding sites. The Primer Database will also store tails and allow you to specify…
-
RNASeq Expression Analysis with NGS data
Read more: RNASeq Expression Analysis with NGS dataIf you have the Assembler module, MacVector can align millions of NGS reads from RNASeq experiments against large genomes and generate a coverage table displaying the relative expression levels of every gene in a genome. The key to this functionality is that you must have a reference genome with genes annotated as CDS or gene…
