Sequence header
(max 100 characters)
Protein sequence *
(max 2000 amino acids, no header)
Email (optional)
Email subject
(max 100 characters)
Comments
(max 200 characters)
Preset parameters:

High recall: We require only 1 orthology method to support an enclosing clade of proposed orthologs. Candidate orthologs can have lower sequence identity and alignment overlap to the query. This parameterization is designed to retrieve more distant orthologs (from distantly related species) but may result in the inclusion of paralogs.
Creating FAT-CAT Job...

Advanced: Modify parameters manually

The stages of the FAT-CAT pipeline are described in detail here.

Stage 1 Parameters: Family HMM Searches

These parameters control the precision and recall of Stage 1 family HMM searches.

Family HMM E-Value  
Fraction of the query that matches an HMM
MDA HMMs %
Fraction of the HMM that matches the query
MDA HMMs %
Pfam HMMs %

Ellis Island Parameters

Hit Coverage %
Query Coverage %
Maxseqs  
Maxfams  
Within-taxon clustering % ID %

Stage 2 Parameters: Subtree HMM scoring and phylogenetic placement

These parameters control the precision and recall of Stage 2 subtree HMM searches and the definition of the Enclosing Clade of presumed orthologs.

Stage 2.1: Subtree HMM Searches
Subtree HMM E-Value  
Stage 2.2: Subtree HMM alignment evaluation
Fraction of the query that matches an HMM
MDA HMMs %
Fraction of the HMM that matches a query
MDA HMMs %
Pfam HMMs %
Minimum % ID between query
and subtree HMM consensus
%

Stage 2.3: Enclosing Clade Criteria

Expand the TSN to the largest Enclosing Clade supported by orthology methods selected below.

For highest precision, check all orthology methods, and require all to support and Enclosing Clade.

For highest recall, check all orthology methods, and require 1 to support an Enclosing Clade.

Require any of the following orthology method(s) to support an Enclosing Clade:

, threshold:

% identity

Stage 2.4: Gathering Enclosing Clade Members
Analyze top sequences for orthology (ordered by similarity to the query)

Stage 3 Parameters: Ortholog selection and tree construction

Stage 3.1: Query-Candidate Ortholog Alignment Analysis
Minimum % ID between
query and candidate ortholog
%
Query Coverage %
Candidate ortholog Coverage %
Stage 3.2: Candidate Ortholog Clustering
Cluster subtrees from one taxon with greater than % identity
Stage 3.3: Displaying Tree
Limit tree display to sequences around the query

Stage 4 Parameters: Derive predicted function

Stage 4.1: Consensus UniProt Description
Exponential decay λ  
Threshold for high confidence  
Threshold for medium confidence