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

Pertea, Geo; Huang, Xiaoqiu; Feng, Liang; Antonescu, Valentin; Sultana, Răzvan; Karamycheva, Svetlana; Lee, Yuandan; White, Joseph A.; Cheung, Foo; Parvizi, Babak; Tsai, Jennifer; Quackenbush, John

doi:10.1093/bioinformatics/btg034

Cited by 1,717 publications

(1,251 citation statements)

References 5 publications

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“…Using the Trinity assembler, 242,069 contigs were obtained with 156.6‐Mb total bases, a 647‐bp average length, and a 943‐bp N50; in addition, 113,359 contigs had a length of more than 400 bp (Figure 2). We performed clustering contigs using TGICL (Pertea et al., 2003), and 190,473 unique clusters were generated with 129.2‐Mb total bases, a 679‐bp average length, and 1,060‐bp N50 size (Table 1, Figure 1). The raw RNA‐Seq reads and assembled transcripts were deposited in the European Nucleotide Archive under the project ID PRJEB19675 and accession numbers HAGJ01000001 to HAGJ01190473 for the assembled transcripts.…”

Section: Resultsmentioning

confidence: 99%

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De novo assembly and characterization of the Hucho taimen transcriptome

Tong

Xü

Zhang

et al. 2017

Ecology and Evolution

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Taimen (Hucho taimen) is an important ecological and economic species that is classified as vulnerable by the IUCN Red List of Threatened Species; however, limited genomic information is available on this species. RNA‐Seq is a useful tool for obtaining genetic information and developing genetic markers for nonmodel species in addition to its application in gene expression profiling. In this study, we performed a comprehensive RNA‐Seq analysis of taimen. We obtained 157 M clean reads (14.7 Gb) and used them to de novo assemble a high‐quality transcriptome with a N50 size of 1,060 bp. In the assembly, 82% of the transcripts were annotated using several databases, and 14,666 of the transcripts contained a full open reading frame. The assembly covered 75% of the transcripts of Atlantic salmon and 57.3% of the protein‐coding genes of rainbow trout. To learn about the genome evolution, we performed a systematic comparative analysis across 11 teleosts including eight salmonids and found 313 unique gene families in taimen. Using Atlantic salmon and rainbow trout transcriptomes as the background, we identified 250 positive selection transcripts. The pathway enrichment analysis revealed a unique characteristic of taimen: It possesses more immune‐related genes than Atlantic salmon and rainbow trout; moreover, some genes have undergone strong positive selection. We also developed a pipeline for identifying microsatellite marker genotypes in samples and successfully identified 24 polymorphic microsatellite markers for taimen. These data and tools are useful for studying conservation genetics, phylogenetics, evolution among salmonids, and selective breeding for threatened taimen.

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Section: Resultsmentioning

confidence: 99%

“…A parameter kmer size of 25 and a depth of at least two kmer were used for assembly with the Trinity package. The contigs resulting from Trinity were further fed to the TGI clustering Tool (version 2.1) (Pertea et al., 2003) to process alternative splicing and redundant sequences.…”

Section: Methodsmentioning

confidence: 99%

De novo assembly and characterization of the Hucho taimen transcriptome

Tong

Xü

Zhang

et al. 2017

Ecology and Evolution

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“…In order to eliminate redundant sequences and improve the sequence quality, the TIGR Gene Indices Clustering Tools (TGICL) [29] was used to obtain consensus sequences from overlapping clusters of ESTs. Assembly criteria included a 50 bp minimum match, 95% minimum identity in the overlap region and 20 bp maximum unmatched overhangs.…”

Section: Resultsmentioning

confidence: 99%

“…These ESTs were assembled using the TGICL program [29]. A Perl script known as MIcroSAtellite (MISA http://pgrc.ipk-gatersleben.de/misa/) was used to mine microsatellites.…”

Section: Methodsmentioning

confidence: 99%

Characterization and development of EST-derived SSR markers in cultivated sweetpotato (Ipomoea batatas)

et al. 2011

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BackgroundCurrently there exists a limited availability of genetic marker resources in sweetpotato (Ipomoea batatas), which is hindering genetic research in this species. It is necessary to develop more molecular markers for potential use in sweetpotato genetic research. With the newly developed next generation sequencing technology, large amount of transcribed sequences of sweetpotato have been generated and are available for identifying SSR markers by data mining.ResultsIn this study, we investigated 181,615 ESTs for the identification and development of SSR markers. In total, 8,294 SSRs were identified from 7,163 SSR-containing unique ESTs. On an average, one SSR was found per 7.1 kb of EST sequence with tri-nucleotide motifs (42.9%) being the most abundant followed by di- (41.2%), tetra- (9.2%), penta- (3.7%) and hexa-nucleotide (3.1%) repeat types. The top five motifs included AG/CT (26.9%), AAG/CTT (13.5%), AT/TA (10.6%), CCG/CGG (5.8%) and AAT/ATT (4.5%). After removing possible duplicate of published EST-SSRs of sweetpotato, a total of non-repeat 7,958 SSR motifs were identified. Based on these SSR-containing sequences, 1,060 pairs of high-quality SSR primers were designed and used for validation of the amplification and assessment of the polymorphism between two parents of one mapping population (E Shu 3 Hao and Guang 2k-30) and eight accessions of cultivated sweetpotatoes. The results showed that 816 primer pairs could yield reproducible and strong amplification products, of which 195 (23.9%) and 342 (41.9%) primer pairs exhibited polymorphism between E Shu 3 Hao and Guang 2k-30 and among the 8 cultivated sweetpotatoes, respectively.ConclusionThis study gives an insight into the frequency, type and distribution of sweetpotato EST-SSRs and demonstrates successful development of EST-SSR markers in cultivated sweetpotato. These EST-SSR markers could enrich the current resource of molecular markers for the sweetpotato community and would be useful for qualitative and quantitative trait mapping, marker-assisted selection, evolution and genetic diversity studies in cultivated sweetpotato and related Ipomoea species.

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“…The ESTs were then clustered using The Institute for Genomic Research Gene Indices clustering tools (TGICL) (Pertea et al 2003) (available from http://www.tigr.org/tdb/tgi/software/). ESTs were clustered if they shared more than 30 bp of at least 95% identity.…”

Section: Methodsmentioning

confidence: 99%

Bioinformatic discovery and initial characterisation of nine novel antimicrobial peptide genes in the chicken

et al. 2004

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Antimicrobial peptides (AMPs) are essential components of innate immunity in a range of species fromDrosophila to humans and are generally thought to act by disrupting the membrane integrity of microbes. In order to discover novel AMPs in the chicken, we have implemented a bioinformatic approach that involves the clustering of more than 420,000 chicken expressed sequence tags (ESTs). Similarity searching of proteinspredicted to be encoded by these EST clusters-for homology to known AMPs has resulted in the in silico identification of full-length sequences for seven novel gallinacins (Gal-4 to Gal-10), a novel cathelicidin and a novel liver-expressed antimicrobial peptide 2 (LEAP-2) in the chicken. Differential gene expression of these novel genes has been demonstrated across a panel of chicken tissues. An evolutionary analysis of the gallinacin family has detected sites-primarily in the mature AMP-that are under positive selection in these molecules. The functional implications of these results are discussed.

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

Cited by 1,717 publications

References 5 publications

De novo assembly and characterization of the Hucho taimen transcriptome

De novo assembly and characterization of the Hucho taimen transcriptome

Characterization and development of EST-derived SSR markers in cultivated sweetpotato (Ipomoea batatas)

Bioinformatic discovery and initial characterisation of nine novel antimicrobial peptide genes in the chicken

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