chromatiblock | Colinear block visualisation tool | Genomics library

chromatiblock is a Python library typically used in Artificial Intelligence, Genomics applications. chromatiblock has no bugs, it has no vulnerabilities, it has build file available, it has a Strong Copyleft License and it has low support. You can download it from GitHub.

An example of a global alignment of 28 complete C. difficile genomes is shown in the above figure. TOP) The global alignment view shows the arrangement of core blocks (i.e. syntenic regions found once in all genomes) in the alignment and how non-core blocks (i.e syntenic regions found in 2 or more genomes) and unique sequences (i.e. sequence found in a single genome) are arranged relative to the core blocks. Core blocks are aligned according to their arrangement in the first genome. The color of the core blocks for each genome is determined by its position. Between any two adjacent core blocks there exists a combination of non-core blocks and unique sequence. This combination is grouped and positioned between the two core blocks to which they are adjacent. In instances where the group cannot be placed between its two adjacent core blocks it is placed arbitrarily next to one of the core blocks to which it is adjacent. This is indicated by removing the gap between core and non-core blocks. In top panel of the above figure a large inversion can be observed in the third isolate from the top, indicated by a difference in ordering of core block colors relative to the reference. Plasmids, found in 9 genomes, consist entirely of non-core and unique blocks. They are positioned on the right side of the figure. BOTTOM) The alignment difference view shows the presence and absence of all non-core blocks.Each genome is represented as a row and each non-core block is assigned a column in the order they are most commonly found in the genome. Presence of each non-core block is shown as a patterned rectangle in the genomes row. As non-core blocks may be present more than once, duplicates are shown by splitting the blocks according to repeat number. Blocks are coloured by user provided categories. This example shows that the main C. difficile pathogenicity locus (PaLoc) that contains the genes encoding the TcdA enterotoxin and TcdB cytotoxin, has been lost in the sixth isolate from the bottom. Six isolates also contain a transposon carry-ing the erm(B) gene, encoding a 23S rRNA methyltransferase that confers resistance to erythromycin. The erm(B)gene is also present in the seventh isolate from the bottom, but located on a novel transposon and inserted elsewhere in the genome.