diff --git a/README.md b/README.md index df924e9..08b3599 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,6 @@ ## Introduction The online BLAST (https://blast.ncbi.nlm.nih.gov) makes dot plots which look like this:

- +

Unfortunately, the *standalone* BLAST lacks the capability of making dot plots. I have made a tool named **Dot_plot_like_in_BLAST** specifically for this purpose. Basically, it is a standalone tool that aligns by BLAST two nucleotide sequences and makes a dot plot. The main differences from the online BLAST are:
1) While the online BLAST always makes rectangular images with 2:1 aspect ratio, the aspect ratio in Dot_plot_like_in_BLAST is equal to the ratio of sequences' lengths. In other words, Dot_plot_like_in_BLAST doesn't distort lengths.
@@ -8,10 +8,10 @@ Unfortunately, the *standalone* BLAST lacks the capability of making dot plots. 3) Dot_plot_like_in_BLAST has several options for image customization. For example, it allows to change the font size and line width.
4) The online BLAST make images in PNG. Dot_plot_like_in_BLAST makes images in PNG, SVG, and also it makes interactive files in HTML. In that interactive files you can magnify a region of interest and save an SVG file specifically for this region.

-This is how an image made by Dot_plot_like_in_BLAST looks. It was made for the same sequences as the image above. - +This is how an image made by Dot_plot_like_in_BLAST looks. It was made for the same sequences as the image above.


+


An example of interactive image manipulation (a region is magnified and saved as a separate SVG file): - + ## How to install Dot_plot_like_in_BLAST has two prerequisites:
@@ -48,4 +48,4 @@ For example, with the following settings the calculation will be faster than wit 3) How does Dot_plot_like_in_BLAST depict indels?
Just as in the online BLAST, indels (gaps in the alignment) are depicted by gaps in the diagram.
For example, here is an alignment (a part of a much longer alignment) and a corresponding diagram:
-
+