Comparative gene analysis

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[]

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

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

Comparative gene analysis
Version 1

Inputs

Steps

Outputs

Version History

2 (earliest) Created 22nd Apr 2024 at 10:50 by Helena Rasche

Creator

Submitter

Comparative gene analysis Version 1

Inputs

Steps

Outputs

Version History

2 (earliest) Created 22nd Apr 2024 at 10:50 by Helena Rasche

Creator

Submitter

Related items

Comparative gene analysis
Version 1