CAETANO, A. R.

CAPRERA, A.

LAZZARI, B.

MARIANI, P.

MERELLI, I.

STELLA, A.

English

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Vol. 23 no. 8 2007, pages 1043–1045BIOINFORMATICS APPLICATIONS NOTE doi:10.1093/bioinformatics/btm063Databases and ontologiesGoSh: a web-based database for goat and sheep EST sequencesAndrea Caprera1,, Barbara Lazzari1, Alessandra Stella1, Ivan Merelli2,Alexandre R. Caetano3 and Paola Mariani11Parco Tecnologico Padano, Via Einstein – Località Cascina Codazza, 26900 Lodi, 2Istituto Tecnologie Biomediche,Via Fratelli Cervi 93, 20090 Segrate (MI), Italy and 3Embrapa Recursos Geneticos e Biotecnologia Parque EstacaoBiologica, Final Av. W/5 Norte, Brasilia-DF, C.P. 02372 70770-900, BrasilReceived on October 25, 2006; revised on February 5, 2007; accepted on February 16, 2007Advance Access publication March 24, 2007Associate Editor: Alfonso ValenciaABSTRACTSummary: The GoSh database is a collection of 58 990 Capra hircusand Ovis aries expressed sequence tags. A perl pipeline wasprepared to process sequences, and data were collected in aMySQL database. A PHP-based web interface allows browsing andquerying the database. Putative single nucleotide polymorphism(SNP) detection, as well as search to repeats were performed, andlinks to external related resources were provided. Sequences wereannotated against three different databases and an algorithm wasimplemented to create statistics of the distribution of retrievedhomologous ontologies in the Gene Ontology categories. The GoShdatabase is a repository of data and links related to goat and sheepexpressed genes.Availability: The GoSh database is available at http://www.itb.cnr.it/gosh/Contact: andrea.caprera@tecnoparco.orgExpressed sequence tags (EST) represent one of the mostimportant sources of information in gene expression studies,however, raw EST sequences must be annotated before they areof value to the research community. The main function of webresources based on organism-specific collections is to providean overview on the distribution of expressed genes in thevarious tissues/organs or in different developmental stages.The aim of the present work was to create a comprehensivedatabase dedicated to goat and sheep, encompassing dataderived from sequence analysis as well as links to relatedonline resources.An analysis pipeline integrating public programs with Perlscripts was created to process 637 goat (Capra hircus) and 58 353sheep (Ovis aries) sequences downloaded from GenBank. TheAutoSNP program, version 7 (Barker et al., 2003), was used toidentify putative single nucleotide polymorphisms (SNPs)in assembled sequences. AutoSNP integrates TGICL (Perteaet al., 2003) that performs sequence clustering and in turnintegrates CAP3 (Huan and Madan, 1999) for contig assembly.Data obtained during the assembly procedure were usedto establish a unigene dataset of 20 784 sequences. All theEST sequences, as well as all the contig consensus sequences,were annotated against three different databases. Two of theseannotation procedures were carried out by BLASTx (Altschulet al., 1990) the former versus the GenBank nr database(referred to as ‘NCBI blast’ in the cited web interface), and thelatter versus the UniProtKB database (http://www.ebi.ac.uk/uniprot/) (referred to as ‘GO blast’ in the cited web interface).A third supplementary annotation was performed by BLASTnagainst an in-house prepared database encompassing 7437 goatand sheep genomic sequences downloaded from GenBank(named ‘genomic blast’ in the cited web interface). All theannotations will be periodically updated and the last updateis indicated at the bottom of the Home Page of the GoSh website. Analysis of repeats was performed with Tandem RepeatsFinder (Benson, 1999). FrameFinder (http://bioweb.pasteur.fr/docs/man/man/ESTate.1.html) was used to infer the mostprobable polypeptide sequence from each EST and contigconsensus sequence. For this purpose, a word probabilityfile was prepared from 45 753 bovidae mRNA sequencesdownloaded from the GenBank CoreNucleotide database.The derived polypeptide sequences were compared to thePROSITE database (Falquet et al., 2002) with scanPROSITE(Gattiker et al., 2002) to retrieve homologous protein patternsand domains. Significantly homologous ‘NCBI blast’ hits werescanned for the presence of EC numbers. When present, thesewere used to retrieve links to the ExPASy NiceZyme pages(http://au.expasy.org/) and to the KEGG pathways database(http://www.genome.jp/kegg/pathway.html). Based on datacontained in the database of associations among proteins andGO elements (www.ebi.ac.uk/GOA), a Perl script was devel-oped to relate GoSh ‘GO blast’ best blast hits to Gene Ontologycategories (The Gene Ontology Consortium, 2000). Matchingontologies were stored into the database to allow a successivedynamic creation of statistics for the ontology occurrences.Links to the AmiGO web pages (http://www.godatabase.org/)were associated to GO terms in the GO Statistics pages. Fulldetails on programs and parameters used in the GoSh database(db) pipeline are available at the Processing, Assembly andAnnotation page of the web site.The Perl pipeline has a modular structure and fills in tables ofa MySQL database. The web interface is based on the PHP*To whom correspondence should be addressed. 2007 The Author(s)This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.Downloaded from https://academic.oup.com/bioinformatics/article-abstract/23/8/1043/199378by Empresa Brasileira de Pesquisa Agropecuaria (EMBRAPA) useron 28 May 2018language, and manages all the incoming queries as well as allthe graphical outputs dynamic creation (Fig. 1).Three interfaces were set up to query the database andretrieve user-defined sequence subsets: the sequence/contigreport tables, the Text Search utility and the Local Blast utility.The sequence/contig report tables report all significant infor-mation related to each sequence/contig. Details on features,BLAST outputs or contig alignments can be accessed via thelinks given in these tables or via the single sequence/contigpages that were assigned to each sequence/contig. The textsearch utility is structured to perform combined keywordsearches on all the fields of the Sequence/Contig reporttables. Searches can be restricted to sequence subsets (goat/sheep, unigenes/not unigenes, singlets/contig-related sequences,putative SNP- or repeats-containing sequences). Query outputscan be downloaded both as multifasta sequence files and intabular format. The local blast interface allows users to blasttheir own sequences against either the nucleic GoSh db datasetor the derivative putative protein database.The GoSh db proved to be very useful for the selection ofsequences to be used for specific purposes (i.e. SNP mapping),and it is currently implemented by the authors in a SNPvalidation and biodiversity study. In particular, the possibilityto use the dataset performing subset-specific text searches offersan efficient tool for data mining and data retrieval.The modular nature of the Perl pipeline and of the PHP-based web interface components, allowed using the samestructures for different projects, adding or removing modulesto perform sequence analyses according to the needs ofdifferent datasets (Lazzari et al., 2005 and unpublished data).Other online databases that were produced by the authors arebased on similar sequence analysis pipelines, but some ofthe features that are presented in this article were created onpurpose for the GoSh database. This is the case, for example,of the package of scripts that were prepared to infer statisticson Gene Ontologies from GO annotations. If applicable,new modules are transferred to the other databases, giving theauthors the opportunity to maintain all the databases upgradedand to improve information related to the different datasetsthey represent.ACKNOWLEDGEMENTSThis work was supported by Fondazione CARIPLO(N 2003.0721/11.8094) and European Specific SupportAction Bioinfogrid (FP6-026808). We acknowledge Dr DaveEdwards and Dr Gary Barker for providing the AutoSNPprogram, Dr Luciano Milanesi, CNR-ITB and L.I.T.B.I.O. forinformatics support and Prof. Francesco Salamini for criticalreading of the manuscript. Funding to pay the Open Accesspublication charges was provided by Parco TecnologicoPadano.Conflict of Interest: none declared.Fig. 1. The GoSh database web interface: an example of a single contig page.A.Caprera et al.1044Downloaded from https://academic.oup.com/bioinformatics/article-abstract/23/8/1043/199378by Empresa Brasileira de Pesquisa Agropecuaria (EMBRAPA) useron 28 May 2018REFERENCESAltschul,S.F. et al. (1990) Basic local alignment search tool. J. Mol. Biol., 215,403–410.Barker,G. et al. (2003) Redundancy based detection of sequence polymorphismsin expressed sequence tag data using autoSNP. Bioinformatics, 19, 421–422.Benson,G. (1999) Tandem repeats finder: a program to analyze DNA sequences.Nucleic Acid Res., 27, 573–580.Falquet,L. et al. (2002) The PROSITE database, its status in 2002. Nucleic AcidsRes., 30, 235–238.Gattiker,A. et al. (2002) ScanPROSITE: a reference implementation of aPROSITE scanning tool. Appl. Bioinformatics, 1, 107–108.Huan,X. and Madan,A. (1999) CAP3: a DNA sequence assembly program.Genome Res., 9, 868–877.Lazzari,B. et al. (2005) ESTree db: a tool for peach functional genomics. BMCBioinformatics, 6 (Suppl. 4:S16), PMID: 16351742.Pertea,G. et al. (2003) TIGR gene indices clustering tools (TGICL): a softwaresystem for fast clustering of large EST datasets. Bioinformatics, 19, 651–652.The Gene Ontology Consortium (2000) Gene Ontology: tool for the unificationof biology. Nature Genet., 25, 25–29.A web-based database for goat and sheep EST sequences1045Downloaded from https://academic.oup.com/bioinformatics/article-abstract/23/8/1043/199378by Empresa Brasileira de Pesquisa Agropecuaria (EMBRAPA) useron 28 May 2018

GoSh: a web-based database for goat and sheep EST sequences.

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GoSh: a web-based database for goat and sheep EST sequences.

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