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: BLAST

Downloading hits from the MacVector 15.5 BLAST Map results tab

The MacVector 15.5 BLAST Map results tab is a unique interface for examining the annotations around hits to a query sequence. Each pane in the display represents a High Scoring Segment Pair, as seen in the BLAST Aligned Sequence tab. At the lower left corner of each pane is a Download button – when you […]

Posted in Tips | Also tagged , | Leave a comment

Use the BLAST Map to better identify blast hits

With the advent of cheap Next Generation Sequencing technologies, there has been an explosion of whole genome sequences deposited in BLAST databases. One consequence of this is that, particularly for sequences of bacterial origin, most of the significant hits are to entire genomes. The classic BLAST results show the sequence alignments, but give no indication […]

Posted in Techniques, Tips | Also tagged , | Leave a comment

Using BLAST to automatically annotate a sequence

You can use the Database->Auto-Annotate Sequence function to quickly annotate a bare sequence using existing annotated sequences on your file system. However, this only works if your collection of sequences contains features representing all parts of the bare sequence. Luckily, if you have an unannotated region after running Auto-Annotate, you can use MacVector’s built-in BLAST […]

Posted in Tips | Also tagged , | Comments closed

Use the BLAST Map to better identify blast hits

With the advent of cheap Next Generation Sequencing technologies, there has been an explosion of whole genome sequences deposited in BLAST databases. One consequence of this is that, particularly for sequences of bacterial origin, most of the significant hits are to entire genomes. The classic BLAST results show the sequence alignments, but give no indication […]

Posted in Tips | Also tagged | Comments closed

MacVector 15.5 is out: Graphical BLAST and automatic ORF display.

Our latest release, MacVector 15.5, introduces an entirely new way to view the results of BLAST searches, with an interactive graphical interface that let’s you easily visualize where your query maps to a hit. Unannotated Open Reading Frames are now automatically displayed whenever you open a DNA sequence. A number of changes to the Align […]

Posted in Uncategorized | Also tagged , , , | Comments closed

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 | Also tagged | Comments closed

IMPORTANT SERVICE ANNOUNCEMENT Entrez and BLAST services will stop working in November for MacVector 15.0.3 and earlier.

UPDATE – November 8, 2016 – Although the official switch off date is not until Wednesday the 9th, Entrez and BLAST are NOT currently working from MacVector 15.0.3 and earlier. We suspect this change is now permanent. UPDATE – November 7, 2016 – We have just been notified by the NCBI that they will be […]

Posted in Releases | Also tagged , | Comments closed

Downloading BLAST Hits from the NCBI direct to your desktop

When you use MacVector to run a BLAST search, did you know that you can download any matching sequences directly from the BLAST Description List window? Simply select text on any part of the line(s) representing the sequence you want to download and choose Database | Retrieve To Desktop or Database | Retrieve To Disk […]

Posted in Techniques, Tips | Also tagged | Comments closed

Using BLAST to automatically annotate a sequence

You can use the Database->Auto-Annotate Sequence function to quickly annotate a bare sequence using existing annotated sequences on your file system. However, this only works if your collection of sequences contains features representing all parts of the bare sequence. Luckily, if you have an unannotated region after running Auto-Annotate, you can use MacVector’s built-in BLAST […]

Posted in Uncategorized | Also tagged , | Comments closed

101 things you (maybe) didn’t know about MacVector: #45 – Automatically annotating sequences using BLAST

The Database | Auto-annotate Sequence… tool is a great way to automatically annotate a bare DNA sequence. If you are unfamiliar with this, check out this previous tip. Auto-annotate is an incredibly simple (and fast!) way to annotate a bare sequence, but it does rely on you having a folder full of sequences containing all […]

Posted in 101 Tips | Also tagged | Comments closed