Comparative gene analysis
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Download RO-CrateWorkflows for comparison of genes in annotated genomes
Associated Tutorial
This workflows is part of the tutorial Comparative gene analysis, available in the GTN
Thanks to...
Tutorial Author(s): Anton Nekrutenko
Workflow Author(s): Anton Nekrutenko
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| Diamond makedb | Diamond makedb | Diamond DB created from ORF predicted from genomes used in the analysis |
|
| Exons | Exons | Amino acid sequences of CDS exons from the gene of interest |
|
| ORFipy BED | ORFipy BED | BED dataset containing information about ORFs predicted in genomes of interest |
|
Steps
| ID | Name | Description |
|---|---|---|
| 3 | Diamond: Find hits in ORFs | Align query against ORF translations toolshed.g2.bx.psu.edu/repos/bgruening/diamond/bg_diamond/2.0.15+galaxy0 |
| 4 | Column Regex Find And Replace | Parse name filed (column 4) pf the BED generated by ORFipy to extract name and frame information. The result has 7 columns thus is not in BED format. The next step reshuffles columns to restore BED. toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.1 |
| 5 | Alignments | Generate tabular view of alignments toolshed.g2.bx.psu.edu/repos/bgruening/diamond/bg_diamond_view/2.0.15+galaxy0 |
| 6 | Cut | Set ORF name as the name and frame as score to reestablish BED format Cut1 |
| 7 | Alignments + BED | Join tabular view of alignments with BED description of individual ORFs. This is necessary because to visualize genes we will need genomic coordinates. join1 |
| 8 | Cut | Extract genomic coordinates of matching ORFs Cut1 |
| 9 | Collapse Collection | Final list of all hits toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0 |
| 10 | Intersect | Find all ORFs overlapping amino acid matches toolshed.g2.bx.psu.edu/repos/devteam/intersect/gops_intersect_1/1.0.0 |
| 11 | Filter | Filter1 |
| 12 | Overlapping ORFs | Collapse a collection into a single dataset by adding genome identified as the first column toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0 |
| 13 | Cut | Remove unnecessary columns Cut1 |
| 14 | Compute | Create unique identified by combining genome name and the ORF name. toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0 |
| 15 | Compute | Crete unique ORF id by combining genome identifier with the ORF name toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.6 |
| 16 | Split file | Split dataset by exon. This would create a collection in which toolshed.g2.bx.psu.edu/repos/bgruening/split_file_on_column/tp_split_on_column/0.4 |
| 17 | Report | Final textual report showing matches, their coordinates and their alignments Cut1 |
| 18 | Tabular-to-FASTA | Create amino acid FASTA sequence from aligned segments of exons toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fasta/tab2fasta/1.1.1 |
| 19 | Cut | Removing unnecessary columns for subsequent processing Cut1 |
| 20 | MAFFT | Create multiple alignments of alienable segments of axons toolshed.g2.bx.psu.edu/repos/rnateam/mafft/rbc_mafft/7.489+galaxy0 |
| 21 | Filter: Plus strand matches | Get positive strand matches Filter1 |
| 22 | Filter: Minus strand matches | Get negative strand matches Filter1 |
| 23 | Join neighbors | Compute NJ phylogenetic trees toolshed.g2.bx.psu.edu/repos/iuc/rapidnj/rapidnj/2.3.2 |
| 24 | Compute | Compute genomic coordinates of matches using global coordinates of ORFs and local coordinates of matches within ORFs toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0 |
| 25 | Compute | Compute genomic coordinates of matches using global coordinates of ORFs and local coordinates of matches within ORFs toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0 |
| 26 | Concatenate datasets | cat1 |
| 27 | Compute | Compute match midpoint. It is needed for creating the image. toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0 |
| 28 | Cut | Cut1 |
| 29 | Compute | toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0 |
| 30 | Join two Datasets | Add information about other ORFs in this area. This is done by talking all ORFs in BED format and left joining with coordinates of matched ORFs. As a result we have a sparse table that contains all ORFs surrounding our matches as well as matches themselves. This information is used to generate the final figure. join1 |
| 31 | Mapping report | Cut1 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| Join neighbors on input dataset(s): Calculated distances | Join neighbors on input dataset(s): Calculated distances | n/a |
|
| _anonymous_output_1 | _anonymous_output_1 | n/a |
|
Version History
1.0 (latest) Created 16th Jul 2024 at 14:04 by Helena Rasche
Added/updated 4 files
Open
master6c8f85e
2.0 (earliest) Created 25th Jun 2024 at 11:06 by Helena Rasche
Added/updated 4 files
Frozen
2.04f6ea18
Creators and Submitter
Views: 478 Downloads: 139
Created: 25th Jun 2024 at 11:06
Last updated: 25th Jun 2024 at 11:06
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