TIGR Gene Indices clustering tools (TGICL): a software system for fast clustering of large EST datasets

By Geo Pertea, Xiaoqiu Huang, F. Liang, Valentin Antonescu, R. Sultana, S. Karamycheva, Yuandan Lee, Joseph White, F. Cheung, Babak Parvizi and 2 more. Bioinform., 2003

1,808 citations recorded by the source corpus.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/fe2e492e3ca8ece17f3e750ef33f5c564d829f52

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In Molecular Biology

1. Sitao Wu
2. Beifang Niu
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Citations in the corpus

• Ultrafast clustering algorithms for metagenomic sequence analysis (2012, methodology): “Many methods were also used for clustering expressed sequence tags (ESTs), such as Unigene [32], TIGR Gene Indices [33], d2_cluster [34] and several others [35–37].”
• The genome of Theobroma cacao (2011, neutral): “Cacao chromosome Arabidopsis chromosome C1(1321) A1(63)-A2(85)-A3(69)-A4(116)-A5(64) C2(935) A1(89)-A2(30)-A4(61)-A5(10) C3(1018) A1(70)-A3(17)-A4(63)-A5(130) C4(837) A1(21)-A2(9)-A3(94)-A4(36)-A5(44) C5(820) A1(24)-A2(51)-A3(78)-A5(37) C6(616) A1(59)-A2(15)-A4(66)-A5(26) C7(287) A1(5)-A5(32) C8(605”
• Corset: enabling differential gene expression analysis for de novo assembled transcriptomes (2014, methodology): “Standalone tools based on sequence similarity are also frequently used [27,28], with CD-HIT-EST a popular choice [29,30].”
• Deep Proteomics of the Xenopus laevis Egg using an mRNA-derived Reference Database (2014, positive): “laevisGene Indices version 11 [24, 46], and the de novo assemblies from the wild-type and J line RNA-seq data were combined (ensuring unique identifiers), cleaned and trimmed using SeqClean (http://compbio.”
• Comprehending crystalline β-carotene accumulation by comparing engineered cell models and the natural carotenoid-rich system of citrus (2011, positive): “The cleaned EST dataset was then clustered and assembled using TGICL (Pertea et al., 2003) using default parameters except for specifying 96% identity for CAP3 contig assembly.”
• Analysis of strawberry genes differentially expressed in response to Colletotrichum infection (2006, methodology): “We use the filtering criteria described by (Liang et al. 2000, Pertea et al. 2003) as follows: the minimum length of the overlap (default 40 bp), the minimum percent of identity for the overlap (default 95”
• Using the miraEST assembler for reliable and automated mRNA transcript assembly and SNP detection in sequenced ESTs. (2004, background): “Both the assembler and the automatic editor are separate programs and can run separately, but we view the task of assembly, assembly validation, and finishing to be closely related enough for both parts to include routines from each other (see also Chevreux et al. 1999; Pfisterer and Wetter 1999).”
• Single Nucleotide Polymorphism Discovery in Cultivated Tomato via Sequencing by Synthesis (2012, methodology): “, 2009); TGICL, The Institute for Genomic Research (TIGR) gene indices clustering tools (Pertea et al., 2003); CAP3,”
• Creating a honey bee consensus gene set (2007, methodology): “EST consensus sequences were generated from 78,001 dbEST and Riken ESTs using TGICL [7].”