Hello @tanghaibao @vivekkrish @orionzhou
Recently I have read the literature (https://onlinelibrary.wiley.com/doi/10.1111/jse.12850) and conducted research on LTR- retrotransposon.
In this article, the author made the following image using MCscanX. The image seems to be drawn by the Python version of MCscanX, but the method seems to be the old MCscanX method.
Method:
"2.6 Syntenic LTR retrotransposons analysis
We firstly extracted the coding sequences of all LTR retrotransposons from three
chromosome-level genomes, PN40024, V. ripara and V. amurensis genomes. Then
the coding sequences were translated into amino acid sequences by using TBtools
v1.098 (Chen et al., 2020). Next, multiple sequence alignment inter- and intra-species was performed using blastp of BLAST+ v2.10.1 with ‘-evalue 1e-5,-outfmt 6’ (Camacho et al., 2009), and finally the alignment results were entered
into MCScanX (Wang et al., 2012) with default parameters for syntenic analysis.
The downstream script ‘duplicate_gene_classifier’ was used to classify origins
duplicate LTR retrotransposons into tandem, proximal, dispersed, segmental or
singleton. The number of intra-species syntenic LTR retrotransposons and the
number of inter-species syntenic LTR retrotransposons was dissected by the script
‘dissect_multiple_alignment’. We clustered the LTR retrotransposons shared
among these three genomes according to their syntenic LTR retrotransposons
within each genome (results from MCScanX) using Yifan Hu multilevel layout
algorithm of Gephi v0.9.2 (https://gephi.org/)."
I used the method used by the authors of this article and got something like this:
What's the matter, please? How can I make figures of MCscanX in Python while using MCscanX in Java?
wyim-pgl
commented
1 year ago
Hello @tanghaibao @vivekkrish @orionzhou Recently I have read the literature (https://onlinelibrary.wiley.com/doi/10.1111/jse.12850) and conducted research on LTR- retrotransposon. In this article, the author made the following image using MCscanX. The image seems to be drawn by the Python version of MCscanX, but the method seems to be the old MCscanX method.
Method: "2.6 Syntenic LTR retrotransposons analysis We firstly extracted the coding sequences of all LTR retrotransposons from three chromosome-level genomes, PN40024, V. ripara and V. amurensis genomes. Then the coding sequences were translated into amino acid sequences by using TBtools v1.098 (Chen et al., 2020). Next, multiple sequence alignment inter- and intra-species was performed using blastp of BLAST+ v2.10.1 with ‘-evalue 1e-5,-outfmt 6’ (Camacho et al., 2009), and finally the alignment results were entered into MCScanX (Wang et al., 2012) with default parameters for syntenic analysis. The downstream script ‘duplicate_gene_classifier’ was used to classify origins duplicate LTR retrotransposons into tandem, proximal, dispersed, segmental or singleton. The number of intra-species syntenic LTR retrotransposons and the number of inter-species syntenic LTR retrotransposons was dissected by the script ‘dissect_multiple_alignment’. We clustered the LTR retrotransposons shared among these three genomes according to their syntenic LTR retrotransposons within each genome (results from MCScanX) using Yifan Hu multilevel layout algorithm of Gephi v0.9.2 (https://gephi.org/)."
I used the method used by the authors of this article and got something like this:
What's the matter, please? How can I make figures of MCscanX in Python while using MCscanX in Java?