ESTpass: a web-based server for processing and annotating expressed sequence tag (EST) sequences

Lee, Byung-Wook; Hong, Tao; Byun, Sang Jin; Woo, Taeha; Choi, Yoon Jeong

doi:10.1093/nar/gkm369

Cited by 30 publications

(20 citation statements)

References 28 publications

(22 reference statements)

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“…Numerous EST assembly methods and integrated platforms have been developed and optimized (Lee et al, 2007;Forment et al, 2008). However, by their nature, EST assemblies typically overestimate the number of genes in transcriptome samples.…”

Section: Development Of a Fl-cdna Transcriptome Resource For Conifer mentioning

confidence: 99%

A White Spruce Gene Catalog for Conifer Genome Analyses

et al. 2011

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Several angiosperm plant genomes, including Arabidopsis (Arabidopsis thaliana), rice (Oryza sativa), poplar (Populus trichocarpa), and grapevine (Vitis vinifera), have been sequenced, but the lack of reference genomes in gymnosperm phyla reduces our understanding of plant evolution and restricts the potential impacts of genomics research. A gene catalog was developed for the conifer tree Picea glauca (white spruce) through large-scale expressed sequence tag sequencing and full-length cDNA sequencing to facilitate genome characterizations, comparative genomics, and gene mapping. The resource incorporates new and publicly available sequences into 27,720 cDNA clusters, 23,589 of which are represented by full-length insert cDNAs. Expressed sequence tags, mate-pair cDNA clone analysis, and custom sequencing were integrated through an iterative process to improve the accuracy of clustering outcomes. The entire catalog spans 30 Mb of unique transcribed sequence. We estimated that the P. glauca nuclear genome contains up to 32,520 transcribed genes owing to incomplete, partially sequenced, and unsampled transcripts and that its transcriptome could span up to 47 Mb. These estimates are in the same range as the Arabidopsis and rice transcriptomes. Next-generation methods confirmed and enhanced the catalog by providing deeper coverage for rare transcripts, by extending many incomplete clusters, and by augmenting the overall transcriptome coverage to 38 Mb of unique sequence. Genomic sample sequencing at 8.5% of the 19.8-Gb P. glauca genome identified 1,495 clusters representing highly repeated sequences among the cDNA clusters. With a conifer transcriptome in full view, functional and protein domain annotations clearly highlighted the divergences between conifers and angiosperms, likely reflecting their respective evolutionary paths.

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Section: Development Of a Fl-cdna Transcriptome Resource For Conifer mentioning

confidence: 99%

A White Spruce Gene Catalog for Conifer Genome Analyses

et al. 2011

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“…hgc.jp) then combined with their quality scores, assembled into contigs and annotated using CAP3 (http://genome.cs.mut.edu/ cap/cap3.html), ESTPass (Lee et al, 2007), and ArthropodEST (http://129.130.115.77/e/). EST sequences from the hemocyte cDNA library were compared to GenBank using BLASTn and BLASTp (www.ncbi.nlm.nih.gov).…”

Section: Sequence Analysismentioning

confidence: 99%

“…EST sequences from the hemocyte cDNA library were compared to GenBank using BLASTn and BLASTp (www.ncbi.nlm.nih.gov). Genome ontology identities were determined using ESTPass (Lee et al, 2007), and Blast2GO (www.blast2GO.de). Additional bioinformatic analyses were performed with programs available on the NCBI (www.ncbi.nlm.nih.…”

Section: Sequence Analysismentioning

confidence: 99%

Analysis of ESTs generated from immune-stimulated hemocytes of larval Heliothis virescens

Shelby¹,

Popham²

2009

Journal of Invertebrate Pathology

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“…EGassembler [41] mainly focuses on de novo EST assembly but users must perform base calling and annotation elsewhere. ESTExplorer [42] and ESTpass [43] extend EGassember with additional functional annotations, but these programs lack genome alignment and microarray probe design functionality. Here, we present an alternative EST analysis pipeline, ESTPiper, for research communities.…”

Section: Comparison With Other Existing Est Analysis Programsmentioning

confidence: 99%

ESTPiper – a web-based analysis pipeline for expressed sequence tags

et al. 2009

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Background: EST sequencing projects are increasing in scale and scope as the genome sequencing technologies migrate from core sequencing centers to individual research laboratories. Effectively, generating EST data is no longer a bottleneck for investigators. However, processing large amounts of EST data remains a non-trivial challenge for many. Web-based EST analysis tools are proving to be the most convenient option for biologists when performing their analysis, so these tools must continuously improve on their utility to keep in step with the growing needs of research communities. We have developed a web-based EST analysis pipeline called ESTPiper, which streamlines typical large-scale EST analysis components.

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ESTpass: a web-based server for processing and annotating expressed sequence tag (EST) sequences

Cited by 30 publications

References 28 publications

A White Spruce Gene Catalog for Conifer Genome Analyses

A White Spruce Gene Catalog for Conifer Genome Analyses

Analysis of ESTs generated from immune-stimulated hemocytes of larval Heliothis virescens

ESTPiper – a web-based analysis pipeline for expressed sequence tags

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