See also
Cross-validation by
identity
usearch_global
command
A top-hit identity distribution (THID) is useful for visualizing distances between a set of query sequences, e.g. OTUs, and a reference database used to predict a trait, e.g. an RDP Classifier training set. OTUs with low identities create a challenging problem for prediction algorithms. Reviewing a THID for a set of OTUs gives an indication of whether predictions based on a given reference are likely to be robust.
USEARCH does not currently support generating a THID as an image file; if this would be useful for you, please let me know. However, it is straightforward to make one with the help of a small script.
Run the OTUs against the reference using the usearch_global command, e.g.:
usearch -usearch_global otus.fa -db refdb.fa -strand plus
-id 0.5 \
-maxaccepts 8 -maxrejects 128 -top_hit_only \
-userout hits.txt -userfields query+target+id
Write a script to scan hits.txt. For each hit, round identity to the nearest integer. Count the number of hits for each identity value. Write the counts to a tabbed file and generate a histogram. The example below is a THID for OTUs from a soil sample, colored to indicate the most probable lowest common rank with the NCBI BLAST 16S reference database.
