{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,12,19]],"date-time":"2024-12-19T19:10:13Z","timestamp":1734635413211,"version":"3.32.0"},"reference-count":6,"publisher":"Oxford University Press (OUP)","issue":"5","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2005,3,1]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Summary: ESTminer is a collection of programs that use expressed sequence tag (EST) data from inbred genomes to identify unique genes within gene families. The algorithm utilizes Cap3 to perform an initial clustering of related EST sequences to produce a consensus sequence of a gene family. These consensus sequences are then used to collect all ESTs in the original EST library that are related using BLAST. A redundancy based criterion is applied to each EST to identify reliable unique gene-sequences. Using a highly inbred genome as a source of ESTs eliminates the necessity of computing covariance on each polymorphism to identify alleles of the same gene, thus making this algorithm more streamlined than other alternatives which must computationally attempt to distinguish genes from alleles.<\/jats:p><jats:p>Availability: The programs were written in PERL and are freely available at http:\/\/www.soybase.org\/publication_data\/Nelson\/ESTminer\/ESTminer.html<\/jats:p><jats:p>Contact: \u00a0nelsonrt@iastate.edu<\/jats:p><jats:p>Supplementary information: Figures and dataset can be obtained from: http:\/\/www.soybase.org\/publication_data\/Nelson\/ESTminer\/ESTminer.html<\/jats:p>","DOI":"10.1093\/bioinformatics\/bti075","type":"journal-article","created":{"date-parts":[[2004,11,6]],"date-time":"2004-11-06T01:14:14Z","timestamp":1099703654000},"page":"691-693","source":"Crossref","is-referenced-by-count":8,"title":["ESTminer: a suite of programs for gene and allele identification"],"prefix":"10.1093","volume":"21","author":[{"given":"Rex T.","family":"Nelson","sequence":"first","affiliation":[{"name":"USDA-ARS, CICGR Ames, IA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"David","family":"Grant","sequence":"additional","affiliation":[{"name":"USDA-ARS, CICGR Ames, IA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Randy C.","family":"Shoemaker","sequence":"additional","affiliation":[{"name":"USDA-ARS, CICGR Ames, IA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2004,11,5]]},"reference":[{"key":"2023013107224220700_B1","doi-asserted-by":"crossref","unstructured":"Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W., Lipman, D.J. 1997Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res.253389\u20133402","DOI":"10.1093\/nar\/25.17.3389"},{"key":"2023013107224220700_B2","doi-asserted-by":"crossref","unstructured":"Barker, G., Batley, J., O'Sullivan, H.O., Edwards, K.J., Edwards, D. 2003Redundancy based detection of sequence polymorphisms in expressed sequence tag data using autoSNP. Bioinformatics19421\u2013422","DOI":"10.1093\/bioinformatics\/btf881"},{"key":"2023013107224220700_B3","doi-asserted-by":"crossref","unstructured":"Huang, X. and Madan, A. 1999CAP3: a DNA sequence assembly program. Genome Res.9868\u2013877","DOI":"10.1101\/gr.9.9.868"},{"key":"2023013107224220700_B4","doi-asserted-by":"crossref","unstructured":"Parkinson, J., Guiliano, D.B., Blaxter, M. 2002Making sense of EST sequences by CLOBBing them. 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