{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,23]],"date-time":"2025-10-23T05:17:50Z","timestamp":1761196670007},"reference-count":14,"publisher":"Springer Science and Business Media LLC","issue":"S4","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2005,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n          <jats:sec>\n            <jats:title>Background<\/jats:title>\n            <jats:p>The ESTree db <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" xlink:href=\"http:\/\/www.itb.cnr.it\/estree\/\" ext-link-type=\"uri\">http:\/\/www.itb.cnr.it\/estree\/<\/jats:ext-link> represents a collection of <jats:italic>Prunus persica<\/jats:italic> expressed sequenced tags (ESTs) and is intended as a resource for peach functional genomics. A total of 6,155 successful EST sequences were obtained from four in-house prepared cDNA libraries from <jats:italic>Prunus persica<\/jats:italic> mesocarps at different developmental stages. Another 12,475 peach EST sequences were downloaded from public databases and added to the ESTree db. An automated pipeline was prepared to process EST sequences using public software integrated by in-house developed Perl scripts and data were collected in a MySQL database. A php-based web interface was developed to query the database.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>The ESTree db version as of April 2005 encompasses 18,630 sequences representing eight libraries. Contig assembly was performed with CAP3. Putative single nucleotide polymorphism (SNP) detection was performed with the AutoSNP program and a search engine was implemented to retrieve results. All the sequences and all the contig consensus sequences were annotated both with blastx against the GenBank nr db and with GOblet against the viridiplantae section of the Gene Ontology db. Links to NiceZyme (Expasy) and to the KEGG metabolic pathways were provided. A local BLAST utility is available. A text search utility allows querying and browsing the database. Statistics were provided on Gene Ontology occurrences to assign sequences to Gene Ontology categories.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusion<\/jats:title>\n            <jats:p>The resulting database is a comprehensive resource of data and links related to peach EST sequences. The Sequence Report and Contig Report pages work as the web interface core structures, giving quick access to data related to each sequence\/contig.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1471-2105-6-s4-s16","type":"journal-article","created":{"date-parts":[[2005,12,3]],"date-time":"2005-12-03T19:13:49Z","timestamp":1133637229000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":27,"title":["ESTree db: a Tool for Peach Functional Genomics"],"prefix":"10.1186","volume":"6","author":[{"given":"Barbara","family":"Lazzari","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Andrea","family":"Caprera","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alberto","family":"Vecchietti","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alessandra","family":"Stella","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Luciano","family":"Milanesi","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Carlo","family":"Pozzi","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2005,12,1]]},"reference":[{"key":"731_CR1","unstructured":"The ESTree Interuniversitary Centre[http:\/\/www.itb.cnr.it\/estree\/files\/ESTree_english.pdf]"},{"key":"731_CR2","unstructured":"GDR: genome database for rosaceae[http:\/\/www.mainlab.clemson.edu\/gdr\/ESTsearchPeach.html]"},{"key":"731_CR3","doi-asserted-by":"publisher","first-page":"175","DOI":"10.1101\/gr.8.3.175","volume":"8","author":"B Ewing","year":"1998","unstructured":"Ewing B, Hiller L, Wendl M, Green P: Basecalling of automated sequence traces using phred. I. Accuracy assessment. Genome Research 1998, 8: 175\u2013185.","journal-title":"Genome Research"},{"issue":"12","key":"731_CR4","doi-asserted-by":"publisher","first-page":"1093","DOI":"10.1093\/bioinformatics\/17.12.1093","volume":"17","author":"H-H Chou","year":"2001","unstructured":"Chou H-H, Holmes MH: DNA sequence quality trimming and vector removal. Bioinformatics 2001, 17(12):1093\u20131104. 10.1093\/bioinformatics\/17.12.1093","journal-title":"Bioinformatics"},{"key":"731_CR5","doi-asserted-by":"publisher","first-page":"868","DOI":"10.1101\/gr.9.9.868","volume":"9","author":"X Huan","year":"1999","unstructured":"Huan X, Madan A: CAP3: A DNA sequence assembly program. Genome Research 1999, 9: 868\u2013877. 10.1101\/gr.9.9.868","journal-title":"Genome Research"},{"issue":"19(3)","key":"731_CR6","doi-asserted-by":"publisher","first-page":"421","DOI":"10.1093\/bioinformatics\/btf881","volume":"12","author":"G Barker","year":"2003","unstructured":"Barker G, Batley J, O' Sullivan H, Edwards KJ, Edwards D: Redundancy based detection of sequence polymorphisms in expressed sequence tag data using autoSNP. Bioinformatics 2003, 12(19(3)):421\u2013422. 10.1093\/bioinformatics\/btf881","journal-title":"Bioinformatics"},{"issue":"5","key":"731_CR7","doi-asserted-by":"publisher","first-page":"651","DOI":"10.1093\/bioinformatics\/btg034","volume":"19","author":"B Parvizi","year":"2003","unstructured":"Parvizi B, Pertea G, Huang X, Tsai J, Quackenbush J, Liang F, Antonescu V, Sultana R, Karamycheva S, Lee Y, White J, Cheung F: TIGR Gene Indices clustering tools (TGICL): a software system for fast clustering of large EST datasets. Bioinformatics 2003, 19(5):651\u2013652. 10.1093\/bioinformatics\/btg034","journal-title":"Bioinformatics"},{"key":"731_CR8","doi-asserted-by":"publisher","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","volume":"215","author":"SF Altschul","year":"1990","unstructured":"Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ: Basic local alignment search tool. J Mol Biol 1990, 215: 403\u2013410. 10.1006\/jmbi.1990.9999","journal-title":"J Mol Biol"},{"key":"731_CR9","unstructured":"mpiBLAST project[http:\/\/mpiblast.lanl.gov\/]"},{"key":"731_CR10","doi-asserted-by":"publisher","first-page":"313","DOI":"10.1093\/nar\/gkh406","volume":"32","author":"D Groth","year":"2004","unstructured":"Groth D, Lehrach H, Hennig S: GOblet: a platform for Gene Ontology annotation of anonymous sequence data. Nucleic Acids Research 2004, 32: 313\u2013317. 10.1093\/nar\/gkh406","journal-title":"Nucleic Acids Research"},{"key":"731_CR11","doi-asserted-by":"publisher","first-page":"25","DOI":"10.1038\/75556","volume":"25","author":"The Gene Ontology Consortium","year":"2000","unstructured":"The Gene Ontology Consortium: Gene Ontology: tool for the unification of biology. Nature Genet 2000, 25: 25\u201329. 10.1038\/75556","journal-title":"Nature Genet"},{"key":"731_CR12","unstructured":"ExPASy Proteomics Server[http:\/\/au.expasy.org\/]"},{"key":"731_CR13","unstructured":"KEGG Pathway Database[http:\/\/www.genome.jp\/kegg\/pathway.html]"},{"key":"731_CR14","unstructured":"Lazzari B, Caprera A, Milanesi L, Stella A, Bianchi F, Vecchietti A, Cosentino C, Viotti A, Pozzi C: ESTree DB and ESTuber DB: a fully automated procedure for EST sequence analysis and database management. Proceedings of the XLVIII Italian Soc of Agric Genet \u2013 SIFV-SIGA Joint Meeting: Lecce 15\u201318 September 2004"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-6-S4-S16.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,9,1]],"date-time":"2021-09-01T08:22:50Z","timestamp":1630484570000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-6-S4-S16"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2005,12]]},"references-count":14,"journal-issue":{"issue":"S4","published-print":{"date-parts":[[2005,12]]}},"alternative-id":["731"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-6-s4-s16","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2005,12]]},"assertion":[{"value":"1 December 2005","order":1,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"S16"}}