ESTuber db: an online database for Tuber borchii EST sequences

Abstract

BackgroundThe ESTuber database () includes 3,271 Tuber borchii expressed sequence tags (EST). The dataset consists of 2,389 sequences from an in-house prepared cDNA library from truffle vegetative hyphae, and 882 sequences downloaded from GenBank and representing four libraries from white truffle mycelia and ascocarps at different developmental stages. An automated pipeline was prepared to process EST sequences using public software integrated by in-house developed Perl scripts. Data were collected in a MySQL database, which can be queried via a php-based web interface.ResultsSequences included in the ESTuber db were clustered and annotated against three databases: the GenBank nr database, the UniProtKB database and a third in-house prepared database of fungi genomic sequences. An algorithm was implemented to infer statistical classification among Gene Ontology categories from the ontology occurrences deduced from the annotation procedure against the UniProtKB database. Ontologies were also deduced from the annotation of more than 130,000 EST sequences from five filamentous fungi, for intra-species comparison purposes.Further analyses were performed on the ESTuber db dataset, including tandem repeats search and comparison of the putative protein dataset inferred from the EST sequences to the PROSITE database for protein patterns identification. All the analyses were performed both on the complete sequence dataset and on the contig consensus sequences generated by the EST assembly procedure.ConclusionThe resulting web site is a resource of data and links related to truffle expressed genes. The Sequence Report and Contig Report pages are the web interface core structures which, together with the Text search utility and the Blast utility, allow easy access to the data stored in the database.

Bacteria associated with truffle‐fruiting bodies contribute to truffle aroma

“…Volatile (3) is furthermore strongly induced by the deletion of YAL012W, a putative carbon‐sulfur lyase, suggesting an enzymatic biosynthesis route in yeast (Howell et al ., ). A blast search of YAL012W against 3271 expressed sequence tags of T. borchii (Lazzari et al ., ) did not reveal any match in the white truffle ; this suggests that the latter gene might either not be expressed or might be absent in T. borchii. In the bacterium Chitinophaga Fx7914, volatile (3) is derived from two primary metabolites, homocysteine and pyruvate (Nawrath et al ., ).…”

A comparative gene index for the white sturgeon Acipenser transmontanus

“…Similar pipelines had already been validated in different projects (Lazzari et al, 2005;Caprera et al, 2007;Lazzari et al, 2007); the Sturgeon db pipeline ( Fig. 1) relies on the same backbone structure, but was deeply modified in order to fit the specific needs of this dataset.…”

Version VI of the ESTree db: an improved tool for peach transcriptome analysis

“…The ESTree sequence analysis pipeline (Figure 1 ) has a modular structure suitable for adaptation to different datasets. Similar pipelines, in fact, were used by the authors in other projects, with different datasets [ 4 , 5 ]. The backbone of the pipeline remained as described in Lazzari et al ., 2005 [ 3 ], but new modules were added to accomplish further analyses and existing modules were partially changed to meet new requirements.…”