PhyloProfile

PhyloProfile tool

• Shiny(R)-based
• dynamically visualize and explore multi-layered phylogenetic profiles
• provide several functions for analysis phylogenetic profiles
• available online & standalone

• Main & additional annotation input
• How to prepare input files

Main input

Required information

1. for basic phylogenetic profile:
   • Gene ID of seed protein or ortholog group ID - geneID
   • Taxonomy ID of species having orthologs (ncbi+taxonID, e.g. ncbi7029, ncbi3702) - ncbiID (*)
   • Ortholog ID - orthoID
2. for additional information layers (optionally):
   • Value for first additional information layer - var1
   • Value for second additional information layer - var2

(*) PhyloProfile requires taxonomy IDs in all of input files.

PhyloProfile is provided with a function for searching taxon IDs from a list of taxon names.

Main input

presence/absence pattern + up to 2 additional variables

FASTA format

Sequence header: >geneID|ncbiID|orthoID|var1|var2

Main input

presence/absence pattern + up to 2 additional variables

orthoXML format

supported by OMA, OrthoMCL, InParanoid, Hieranoid, Panther, Roundup, etc.

*Click here for "How to use OMA orthoXML file"

Main input

presence/absence pattern + up to 2 additional variables

long format

tab delimited file containing 5 columns: geneID, ncbiID, orthoID, var1, var2

Main input

presence/absence pattern + up to 2 additional variables

matrix (wide) format

header line contains ncbiID

each cell contains orthoID#var1#var2

NOTE: this format is not suitable for profiles containing paralogs (co-orthologs)

Annotation input (optional)

domain annotations or structural information

Domain file is a tab-liminated file contains:

1. pairID: geneID#orthoID
2. orthoID (required) and seedID: if both are present, domain plot will show domain architectures of both proteins for comparison. Otherwise only domains of orthologs will be plotted.
3. feature name: name of domains
4. start and end postion of each domain in the protein.
5. weight value for each feature (set as NA if unavailable)

How to prepare input files

• Main input:
  1. Use newest version of HaMStR can directly generate compartible profile and domain files for PhyloProfile.
  2. Obtain HOGs from OMA Browser:

     python ./scripts/get_oma_hogs.py -i data/demo/oma/omaIDs.list > data/demo/oma/omaHogs.orthoxml

  3. Convert OMA Standalone:

     python ./scripts/convert_oma_standalone_orthoxml.py -x data/demo/oma/oma_example.orthoxml-m data/demo/oma/taxon_mapping_oma_orthoxml.csv > data/demo/oma_example_phyloprofile_compatible.orthoxml

  4. Download orthoXML file from other supported public databases (if available).
  5. Prepare input file manually by yourself in FASTA, long or matrix format :)

How to prepare input files

• Domain file:
  1. HaMStR can directly generate compartible profile and domain files for PhyloProfile.
  2. Use HMMScan and PfamScan to do PFAM annotation:

     hmmscan -E 0.001 --noali --domtblout hmmscanOut.txt path_to_Pfam-a_files/Pfam-A.hmm data/demo/test.input.fasta

     perl pfamscan.pl -fasta test.input.fasta -dir path_to_Pfam-A_files > pfamscanOut.txt

     then parse output files into compatible domain files:

     python ./scripts/hmmscanParser.py -i data/demo/pfamAnno/hmmscanOut.txt > hmmscanOut.domains

     python ./scripts/pfamscanParser.py -i data/demo/pfamAnno/pfamscanOut.txt > pfamscanOut.domains

  3. Prepare input file manually by following this format.

• Variables
• Configurations
• Seed taxon selection

Variables

• 2 additional information layers
• Use max, min, mean or median values for aggregation

Configurations

• use all genes for analysis or upload list of genes of interest (Choose genes of interest)
• alphabetical order sequences IDs or keep the order as in the input (Order sequence IDs)
• order taxa based on NCBI taxonomy tree or by user-defined tree(*) (Order taxa)
• set path to sequence files (FASTA config)
• change default colors for profile plots (Set colors for profile)

(*) input species tree has to be in newick format and should not contain singletons

Seed taxon selection

higher taxonomic level = more general analysis

Profile appearance

Variable thresholds

dynamically filter profile

Point's info

info of a selected point on the profile

• detailed scores for 2 additional variables
• FASTA sequence of ortholog

Domain architecture plot

for comparing protein architectures