EZcircular

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EZcircular helps users to re-arrange the mitochondrial genome by providing a new starting gene.

EZcircular must be intended to work with MITOS output files , hence use it in according to the following instructions:

1. Prepare a BED file (.bed or .txt) of your mitochondrial genome. Please make sure that:
   • it's a BED file. GFF format will not be detected and the analysis will stop. In case you have a GFF file, convert it (gff2bed should work)
   • the BED file contains 6 fields: 'chrom', 'chromStart', 'chromEnd', 'name', 'score','strand'. The BED file is thaugh to be used as MITOs BED output. Take a look on how a BED file is strucutured here;
   • the annotation file is as complete as possible;
   • if your genome is incomplete, namely is missing of some genes, use the linear option
2. Upload the bed file in the Upload BED link button.
3. Prepare a FASTA file (.fasta, .fa, .fsa, .fas, .fna, .ffn, .faa, .frn) with only ONE sequence corresponding to the reference genome. Please make sure that:
   • it's a FASTA file.
   • it oly contains one sequence corresponding to the reference genome;
   • if your genome is incomplete, namely is missing of some genes, use the linear option
4. Upload the bed file in the Upload BED link button.
5. Upload the bed file in the Upload FASTA link button.
6. Choose between linear or circular option from the dropdown menu.
7. Choose your starting gene
8. If the analysis does not produce errors, a compressed folder will be downloaded. Both input and output files will be stored in the compressed folder.

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Your data will go through the following steps:

1. the bed file will be check. If the format is correct it will pass to the next step
2. if you set up the linear option, 100 Ns will be appended at the end of your reference
3. the starting gene will be searched trough your annotation bed file, picking up its coordinates
4. the fasta file will be re-arranged starting from this position
5. a new BED files with the updated coordinates will be created.

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Download an input FASTA example

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Job name*

Select a .bed (alteratively .txt) file

Select a ..fasta, .fa, .fsa, .fas, .fna, .ffn, .faa, .frn file

Select the feature of your genome circular linear

Select the starting gene from which re-arrange the reference positions- (e.g. cox1)

Upload

*Useful to organize your processed jobs. If not provided, a random ID will be created.