Workflow Type: Galaxy

Workflows 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

gtn star logo followed by the word workflows

Inputs

ID Name Description Type
Diamond makedb Diamond makedb Diamond DB created from ORF predicted from genomes used in the analysis
  • File[]
Exons Exons Amino acid sequences of CDS exons from the gene of interest
  • File
ORFipy BED ORFipy BED BED dataset containing information about ORFs predicted in genomes of interest
  • File[]

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
  • File
_anonymous_output_1 _anonymous_output_1 n/a
  • File

Version History

1.0 (latest) Created 16th Jul 2024 at 14:04 by Helena Rasche

Added/updated 4 files


Open master 6c8f85e

2.0 (earliest) Created 25th Jun 2024 at 11:06 by Helena Rasche

Added/updated 4 files


Frozen 2.0 4f6ea18
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Views: 451   Downloads: 130

Created: 25th Jun 2024 at 11:06

Last updated: 25th Jun 2024 at 11:06

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