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!

101 things you (maybe) didn’t know about MacVector: #44 – Opening matching sequences from an Align To Folder search

The Database | Align To Folder function is an extremely useful tool to help you find matching sequences on your own local file system. It is essentially a BLAST search of your own private sequence collection – a little slower, but more sensitive. You can use it to easily open all of the sequences you have that match a particular sequence. Lets say you have a vector with a Gentamycin resistance gene, and you want to find and retrieve all of the vectors in your collection that have that gene. How about this as your starting vector;

GentRSelected

Select the Gentamycin gene (as shown) and invoke Database | Align To Folder. MacVector will only search using the selected sequence range. Here I chose the MacVector supplied Common Vectors folder as my target, but you can choose any hierarchy of folders where you keep your constructs;

Align to Folder

The results show the best matching sequences, but its obvious from the Map which have perfect matches. You can also examine the Folder Aligned Sequence tab to view the actual alignments and work out which hits are true matches.

PDONR 207 Results

You can select the best matching sequences in the Folder Description List text – note that it is not necessary to select the entirety of the lines containing the sequences you are interested in. When the row(s) are selected, you will find that the Database | Retrieve To Desktop, Database | Retrieve To Disk and Database | Retrieve To File menu options become active.

Align2FolderSelections

Retrieve To Desktop: this option will open all of the selected files directly in MacVector;

GentamycinVectors

Retrieve To Disk: if you choose this option, you will be prompted to select a destination folder. The matching sequence files will be COPIED to this folder.

Retrieve To File: if you choose this option, the sequences will be copied into a single file of the name you choose, in either Fasta or Fastq format. This option is primarily provided to let you retrieve matching reads from large Fasta or Fastq NGS data files.



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