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ITSx Extractor (version 1.0.11)

Input Fasta:

Domain E-value Cutoff:

Domain E-value cutoff a sequence must obtain in the HMMER-based step to be included in the output.

Domain Score Cutoff:

Domain score cutoff that a sequence must obtain in the HMMER-based step to be included in the output.

Minimum Number of Domains:

The minimum number of domains (different HMM gene profiles) that must match a sequence or it to be included in the output (detected as an ITS sequence). Setting the value lower than two will increase the number of false positives, while increasing it above two will decrease ITSx detection abilities on fragmentary data.

HMMER Search Type:

Search E-value:

The actual E-value cutoff used in the HMMER search. High numbers may slow down the process. Should never be set to a lower value than the Domain E-value Cutoff opion. Cannot be used in combination with Search Score option.

Re-creates the HMM-database before ITSx is run:

Allow profiles not to be in the expected order on the extracted sequences:

Check both DNA strands against the database:

Use HMMER's heuristic filtering:

Preserve sequence headers instead of printing out ITSx headers:

Remove ends of ITS sequences if they are outside of the ITS region:

Description

Identifies ITS sequences and extracts the ITS regions.

ITSx is an open source software utility to extract the highly variable ITS1 and ITS2 subregions from ITS sequences, which is commonly used as a molecular barcode for e.g. fungi. As the inclusion of parts of the neighbouring, very conserved, ribosomal genes (SSU, 5S and LSU rRNA sequences) in the sequence identification process can lead to severely misleading results, ITSx identifies and extracts only the ITS regions themselves. For more information regarding the settings of the tool, please visit the ITSx Users Guide on http://microbiology.se/publ/itsx_users_guide.pdf

Inputs and Outputs

Inputs:
- Accepts input in the FASTA format. It is possible to input both aligned and unaligned FASTA files, containing both DNA and RNA sequences
Outputs:
- Summary file of the entire run
- One or more detailed table containing the positions in the respective sequences where the ITS subregions were found
- Semi-graphical representation of hits
- FASTA file of all identified sequences
- FASTA file for ITS1 regions
- FASTA file for ITS2 regions
- A list of sequence IDs representing the entries (if they exist) that did not contain any ITS region
- A file containing chimeric sequences (if they are found)
- A file for problematic sequences

Tool Information

ITSx tool v1.0.11:
- Release Date: December 2014
- URL: http://microbiology.se/software/itsx/
- Source URL: http://microbiology.se/sw/ITSx_1.0.11.tar.gz
- Copyright (C) 2012-2013 Johan Bengtsson-Palme et al.

Contact Information

For more information, contact:
- AAFC-MBB Team
- E-mail: mbb@agr.gc.ca
- Agriculture and Agri-foods Canada, Ottawa, ON, Canada