Examine SH (Species Hypothesis) hits from UNITE database

This tutorial is about how to examine poorly classified fungal OTUS by comparing to SHs from the UNITE database, which often don’t have species names associated with them but are consistent taxa which could be of interest to the user.

This will require a downloaded UNITE database.

You can do this two separate ways:

1. Use the same database for both -d/--db and for --isolates.

   constax \
   -i otus.fasta \
   -b \
   -t \
   -d sh_general_release_fungi_35077_RepS_04.02.2020.fasta \
   --isolates sh_general_release_fungi_35077_RepS_04.02.2020.fasta
   

   The accessions found in the constax_taxonomy.txt file in the output directory is searchable at the UNITE search page.

2. Examine the blast.out file in the directory specified by -x/--tax or the default ./taxonomy_assignments directory.

   # BLASTN 2.10.0+
   # Query: OTU_1
   # Database: /mnt/ufs18/rs-022/bonito_lab/CONSTAX_May2020/UNITE_Fungi_tf/sh_general_release_fungi_35077_RepS_04.02.2020__BLAST
   # Fields: query acc., subject acc., evalue, bit score, % identity, % query coverage per subject
   # 5 hits found
   OTU_1   KC306753        1.04e-96        351     99.482  100
   OTU_1   AF377107        2.25e-93        340     98.446  100
   OTU_1   AF377107        2.25e-93        340     98.446  100
   OTU_1   KC306757        8.16e-88        322     96.891  100
   OTU_1   KC306757        8.16e-88        322     96.891  100
   

The second column is an accession number that can be searched at the UNITE search page.