Galaxy | Tool Preview

Chromeister (version 1.5.a+galaxy1)
Query sequence file in fasta format
Reference sequence file in fasta format
Use around 1000 for chromosome-sized sequences and around 2000 for complete genomes
Use 32 as default, and 16 in case no similarities are found
Level of the heuristic subsampling employed. Change to 1 or 2 if no similarity is found
Do not use grid if your multi-fasta contains more than a hundred sequences (approximately)
If enabled, a png image will be generated showing the detected blocks and classified by color

CHROMEISTER

CHROMEISTER is a heuristic approach for the ultra fast previsualization of pairwise genome comparisons. It is able to compare enormous genomes (up to 30 thousand million base pairs, or 10 times the size of the human genome) much faster than other methods while yielding significant, reusable and exploitable information such as synteny blocks, evolutionary events or pairwise genome similarity metrics.

What is CHROMEISTER good for? It is specially suitable to obtain a fast visualization of a pairwise genome comparison. Due to its unique-seeds filtering, it is particularly useful to inspect noisy, full-of-repeats genome comparisons. Additionally, since it outputs a scoring metric for each comparison, it can be used for massive all vs all comparisons that get automatically processed based on such metric.

What is CHROMEISTER NOT good for? It should NOT be used to obtain alignments. CHROMEISTER, as it is, does not produce a set of alignments (although it can be done using the GECKO pipeline, see github repository). It should also NOT be used to perform studies on DNA repeats, since CHROMEISTER filters these as part of its main signal detection process.

How to use

To use Chromeister, upload two .fasta data sets and select these as "Query sequence" and as "Reference sequence". Once so, choose the parameters that best suite your comparison:

Input parameters

Output data sets