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101 things you (maybe) didn’t know about MacVector: #16 – Using A Primer Database
Read more: 101 things you (maybe) didn’t know about MacVector: #16 – Using A Primer DatabaseIf you have accumulated a collection of primers in your freezer, then you should consider storing the sequences in a primer database within MacVector so that you can rapidly scan any new plasmids for potential primer binding sites. Plus, you’ll have a nice electronic record of all your primer sequences. Start by choosing File |…
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101 things you (maybe) didn’t know about MacVector: #15 – Getting GenBank/Entrez Sequences Into MacVector
Read more: 101 things you (maybe) didn’t know about MacVector: #15 – Getting GenBank/Entrez Sequences Into MacVectorMacVector does have a built-in Entrez browser that lets you search the online Entrez GenBank database using keywords and retrieve matching sequences either To Disk or as sequence windows (To Desktop) without needing to leave MacVector. You can access this via the Database | Internet Entrez Search… menu item. I’m not going to discuss how…
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Multisite Gateway cloning using the Cloning Clipboard
Read more: Multisite Gateway cloning using the Cloning ClipboardWith the introduction of the Cloning Clipboard in MacVector 12.7 both single step and Multisite Gateway cloning can be easily designed, replicated and documented. The Cloning Clipboard allows you to assemble fragments by dragging compatible ends of digested fragments together to form new fragments. Every digest operation in a sequence window will place a fragment…
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101 things you (maybe) didn’t know about MacVector: #14 – How To Align Non-Overlapping Protein Fragments Against A Parent Protein
Read more: 101 things you (maybe) didn’t know about MacVector: #14 – How To Align Non-Overlapping Protein Fragments Against A Parent ProteinThe classic algorithm for aligning multiple protein sequences is ClustalW. Normally, it does a great job of aligning related DNA and Protein sequences and can handle thousands of sequences if required. However, one place where it struggles is if you are aligning non-overlapping segments of DNA or Protein against a parental full-length sequence. The reason…
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101 things you (maybe) didn’t know about MacVector: #13 – Lower Case Sequences
Read more: 101 things you (maybe) didn’t know about MacVector: #13 – Lower Case SequencesBy default, MacVector uses upper case letters for sequence residues. However, you can also use lower case characters if you wish. Changing the case of residues does not affect the MacVector analysis algorithms – GAATTC, gaattc and gAAttC are all considered valid EcoRI sites for example. If you want to set a short region of…
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101 things you (maybe) didn’t know about MacVector: #12 – Displaying Segmented Features
Read more: 101 things you (maybe) didn’t know about MacVector: #12 – Displaying Segmented FeaturesWhile most features you might encounter in DNA files have a simple start and stop location on the sequence, some features are segmented. For example, the coding sequence of a protein encoding reading frame containing introns is represented by a segmented CDS feature on the genomic DNA. MacVector has always understood that the individual segments…
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MacVector Workshops at the NIH
Read more: MacVector Workshops at the NIHMacVector, Inc will be giving two training workshops on the NIH Main Campus tomorrow. Tuesday, September 11, 2012. 10:00 AM – 12:00 AM 1:00 PM – 3:00 PM Sign up for the workshop (no charge) There is still space available for these two MacVector workshops. It is designed for both novice and advanced users. Our…
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101 things you (maybe) didn’t know about MacVector: #11 – What Is The Tm Of My Primer?
Read more: 101 things you (maybe) didn’t know about MacVector: #11 – What Is The Tm Of My Primer?So, you have a primer sequence and you want to know what its melting temperature is? Well, MacVector has a lot of Primer Design functionality, and sometimes its difficult to know where to start. If you have MacVector 12.6 or later, the easiest and quickest way to do this is using the Quicktest Primer functionality.…
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101 things you (maybe) didn’t know about MacVector: #10 – Displaying Amino Acids As Triple Letter Codes In Translations
Read more: 101 things you (maybe) didn’t know about MacVector: #10 – Displaying Amino Acids As Triple Letter Codes In TranslationsFollowing on from my last post about turning on translations in the sequence Editor, I thought I should point out how to display amino acid translations using the 3-letter code rather than the default single-letter code. I don’t know about you, but I have a hard time remembering that “W” is the single-letter IUPAC code…
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101 things you (maybe) didn’t know about MacVector: #9 – Showing Translations In The DNA Sequence Editor
Read more: 101 things you (maybe) didn’t know about MacVector: #9 – Showing Translations In The DNA Sequence EditorIf you have used MacVector for many years, you’ll remember the days when the single sequence editor was THE main way you interacted with MacVector. When MacVector 10 was introduced back in 2007, the Editor became just one tab in the single sequence window along with Map, Features and Annotations tabs, all of which at…
