Graphical Issue On Macvector Nucleic Acid Map Alignments

Question

[Anima Mundi]

Hello, I have a series of MacVector "nucleic acid" genomic sequences. I used each of them as a reference for a series of pairwise alignments of other sequences coming from cDNA sequencing. For some of those genomic sequence alignments, I have a graphic issue: the map of the alignment does not show every cDNA sequence in a different line (that is, the graphical representations of the sequences are not always correctly piled over the line representing the genomic sequence), it overlaps some of them so that the appearance is messy; sometimes there is also empty space between those representations bars of the cDNA sequences. On average, there are 10-15 cDNA sequences aligned on the genomic one. Could it be that there is some kind of space limitation? How could I overcome the problem?

Answer 1

[fergycool]

There's quite a few different ways of creating alignments as you describe in MacVector so I cannot be too specific without more information. However, what you are probably seeing is the tiled mode view of alignments. In MacVector by default most alignments that potentially have thousands/millions of much smaller sequences aligned against a much longer reference sequence or that form a much longer consensus sequence are displayed in non-tiled mode.

With Tiled mode turned on all assembled sequences are displayed on a separate line.

When Tiled mode is turned off, only the assembled sequences that overlap the current visible range are displayed.

Non tiled mode is much easier for visualising a long refererence sequence with many thousands of short sequences aligned against it. Without this option you would mainly get a screen full of white space! For example in non-tiled mode when you scroll along the alignment you will always see aligned sequences.

For the type of alignment that you are doing I would use the Align to Reference editor. This is optimised for the much smaller alignments of the type you describe, i.e. mapping cDNAs to genomic. It also only displays in tiled mode.

• open up your reference sequence and go ANALYZE > ALIGN TO REFERENCE EDITOR

• Click on the "+" button and add your cDNA sequences

• Click the ALIGN button and switch the drop down menu to cDNA. Click ALIGN

I think that I've answered your question correctly but if I've got it completely wrong do let me know (and vote my answer down!).

(Disclaimer: I work for MacVector Support).

Cheers

Chris

[Anima Mundi]

Sorry, this does not answer my question. If I go to the "Analyze" menu, there I find an option called "Align to Reference...". If this is equivalent to "Align to Reference Editor", than the procedure you suggest is exactly the one I used to obtain my alignments. In the meanwhile, I overcame the problem moving some of the sequences below the reference one: of course this is not the optimal solution, but I start to suspect that there is some kind of limitation in the number of cDNA sequence correctly displayable. Searching "tiled" gives no result in the "Help" menu, searching "tile" gives just the "Tile" option, but for the "Window" menu (this moves the working window, I saw). Thanks anyway, bye!

[fergycool]

Sorry I misunderstood your question originally. The Map view dynamically lays out the symbols representing aligned sequences above the sequence for forward ones and below for reverse. However, if you double click an individual symbol you can "fix" where it appears in the Map. That's doable for 15 sequences, however, for larger number of sequences putting an individual sequence on a single line would result in very small symbols or a very large map. The Map is intended as more of an overview of your alignment, with the editor for sequence level. A good tip is to open a Replica window of the Editor and arrange both windows together (use the WINDOW > TILE menu you mention). Then clicking on a symbol in the Map will zoom to and display that region of the sequence in the Editor.