title: ESTminer: a suite of programs for gene and allele identification.
abstract: 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.
  
  
  BACKGROUND
  The programs were written in PERL and are freely available at http://www.soybase.org/publication_data/Nelson/ESTminer/ESTminer.html
  
  
  BACKGROUND
  nelsonrt@iastate.edu
  
  
  BACKGROUND
  Figures and dataset can be obtained from: http://www.soybase.org/publication_data/Nelson/ESTminer/ESTminer.html.
authors.affiliation: USDA-ARS, CICGR Ames, IA, USA. nelsonrt@iastate.edu
authors.forename: Rex T
authors.initials: RT
authors.lastname: Nelson
authors.forename: David
authors.initials: D
authors.lastname: Grant
authors.forename: Randy C
authors.initials: RC
authors.lastname: Shoemaker
mesh_terms: D000465:Algorithms; D002874:Chromosome Mapping / Q000379:methods*; D016384:Consensus Sequence; D003628:Database Management Systems; D030541:Databases, Genetic; D020224:Expressed Sequence Tags; D005787:Gene Frequency / Q000235:genetics*; D006239:Haplotypes / Q000235:genetics; D016247:Information Storage and Retrieval / Q000379:methods*; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods*