A software pipeline for processing and identification of fungal ITS sequences.

ABSTRACT:

Background

Fungi from environmental samples are typically identified to species level through DNA sequencing of the nuclear ribosomal internal transcribed spacer (ITS) region for use in BLAST-based similarity searches in the International Nucleotide Sequence Databases. These searches are time-consuming and regularly require a significant amount of manual intervention and complementary analyses. We here present software - in the form of an identification pipeline for large sets of fungal ITS sequences - developed to automate the BLAST process and several additional analysis steps. The performance of the pipeline was evaluated on a dataset of 350 ITS sequences from fungi growing as epiphytes on building material.

Results

The pipeline was written in Perl and uses a local instal

SUBMITTER: Nilsson RH 

PROVIDER: S-EPMC2649129 | biostudies-literature | 2009 Jan

REPOSITORIES: biostudies-literature