What's this?
Find frameshifted de novo gene.
Workflow
Follow this flow from top to bottom. For further information, please refer to README on each sub directories.
preprocess
- Data acquisition and preprocessing
blastn
- blastn taxonomy restricted gene family to genomes which do not have the family.
analize
- analize
Input Data
MBGD Ortholog Cluster Table with corresponding complete genomes & their annotations.
cluster.tab
| ClusterID | HomClusterID | Size | ...genomes... | Gene | ...params... | Description |
|---|---|---|---|---|---|---|
| 1 | 1 | #genes | ...gene ids... | family name (if exists) | ... | description of family (if exists) |
mbgd_2016-01_gene
annotation file. "from1" & "to1" columns corresponds to [first, last] position.
visualizatio by IGV
- copies .dnaseq
- gets .gff by ./preprocess/convert2gff.py
- gets .igv by MitsukiUsui/genome/patternanalyze/stop_codon_igv.py
- gets .bed by ./blastn/convert2bed.py
- gets .bat by ./analyze/convert2bat.ipynb if needed