Is there any stand alone dot plot program which is like web-based in 'Plant Genome Duplication Database' or CoGE? Maybe dotter is a candidate，but I don't like its interface.
ps:It required whole genome pep blastp hit based plot,not sequence alignment based.
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Liuyunlong •
I use a python script to generate dot plot, for synteny purposes. It depends on a plotting library matplotlib. Incidentally, I am involved in the two projects you mentioned.
Usage:
blast_plot.py blast_file --qbed query.bed --sbed subject.bed
visualize the blast_file in a dotplot
Options:
-h, --help show this help message and exit
--qbed=QBED path to qbed
--sbed=SBED path to sbed
--synteny run a fast synteny scan and display synteny blocks
blast_file is a BLAST tabular output (-m 8 in BLAST or -outfmt 6 in BLAST+). The .bed file has four columns.
chromosome_id start stop gene_name
The gene names in query.bed has to match the names used in the first column in blast_file; names in subject.bed has to match names in the second column in blast_file.
Optionally, flag --synteny will highlight all the syntenic blocks in this dot plot.
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Haibao Tang
Orz,It's very very helpful.And if I want to show MCscan pairwise alignment result rather than a fast synteny scan,what could I do? Or just to transform the MCscan result to blast m8 like format ,is also can meet my job's requirement
It's very very helpful.And if I want to show MCscan pairwise alignment result rather than a fast synteny scan,what could I do? Or just to transform the MCscan result to blast m8 like format ,also can meet my job's requirement，thanks very much.谢谢
Readme of quota-alignment make me understand more clearly:)
The MUMmer package can generate a variety of genome-scale alignments (including translated nucleic acid sequence, using promer). It also has several plotting options: see mummerplot on the examples page for a dotplot-like example.
LAST has a script last-dotplot.py. See also http://last.cbrc.jp/doc/last-scripts.txt and http://last.cbrc.jp/doc/last-manual.txt.
googling for 'dotplot' returns many command-line programs: e.g: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps
EMBOSS alignment dotplot tools: http://emboss.sourceforge.net/apps/cvs/emboss/apps/alignment_dot_plots_group.html
We wrote this small python script: https://pypi.python.org/pypi/dotplot/ which provides both CLI and GUI, although it is sequence based:
Maybe you'll enjoy FlexiDot: It is well documented, implemented in Python and controlled with the commandline. It allows all-against-all, pairwise and self dotplots, and comes with many features, such as
Code on github: http://github.com/molbio-dresden/flexidot
Publication: http://doi.org/10.1093/bioinformatics/bty395
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