TITLE

Generation, annotation, analysis and database integration of 16,500 white spruce EST clusters

PUB. DATE
January 2005
SOURCE
BMC Genomics;2005, Vol. 6, p144
SOURCE TYPE
Academic Journal
DOC. TYPE
Article
ABSTRACT
No abstract available.
ACCESSION #
43683429

 

Related Articles

  • The Diatom EST Database. Maheswari, Uma; Montsant, Anton; Goll, Johannes; Krishnasamy, S.; Rajyashri, K. R.; Patell, Villoo Morawala; Bowler, Chris // Nucleic Acids Research;Jan2005, Vol. 33 Issue suppl 1, pd344 

    The Diatom EST database provides integrated access to expressed sequence tag (EST) data from two eukaryotic microalgae of the class Bacillariophyceae, Phaeodactylum tricornutum and Thalassiosira pseudonana. The database currently contains sequences of close to 30 000 ESTs organized into PtDB,...

  • A hitchhiker's guide to expressed sequence tag (EST) analysis. Nagaraj, Shivashankar H.; Gasser, Robin B.; Ranganathan, Shoba // Briefings in Bioinformatics;Jan2007, Vol. 8 Issue 1, p6 

    Expressed sequence tag (EST) sequencing projects are underway for numerous organisms, generating millions of short, single-pass nucleotide sequence reads, accumulating in EST databases. Extensive computational strategies have been developed to organize and analyse both small- and large-scale EST...

  • ESTpass: a web-based server for processing and annotating expressed sequence tag (EST) sequences. Lee, Byungwook; Hong, Taehui; Byun, Sang Jin; Woo, Taeha; Choi, Yoon Jeong // Nucleic Acids Research;2007, Vol. 35 Issue suppl_2, pW159 

    We present a web-based server, called ESTpass, for processing and annotating sequence data from expressed sequence tag (EST) projects. ESTpass accepts a FASTA-formatted EST file and its quality file as inputs, and it then executes a back-end EST analysis pipeline consisting of three consecutive...

  • annot8r: GO, EC and KEGG annotation of EST datasets. Schmid, Ralf; Blaxter, Mark L. // BMC Bioinformatics;2008, Vol. 9, Special section p1 

    Background: The expressed sequence tag (EST) methodology is an attractive option for the generation of sequence data for species for which no completely sequenced genome is available. The annotation and comparative analysis of such datasets poses a formidable challenge for research groups that...

  • CR-EST: a resource for crop ESTs. Künne, C.; Lange, M.; Funke, T.; Miehe, H.; Thiel, T.; Grosse, I.; Scholz, U. // Nucleic Acids Research;Jan2005, Vol. 33 Issue suppl 1, pd619 

    The crop expressed sequence tag database, CR-EST (http://pgrc.ipk-gatersleben.de/cr-est/), is a publicly available online resource providing access to sequence, classification, clustering and annotation data of crop EST projects. CR-EST currently holds more than 200 000 sequences derived from 41...

  • EST2uni: an open, parallel tool for automated EST analysis and database creation, with a data mining web interface and microarray expression data integration.. Forment, Javier; Gilabert, Francisco; Robles, Antonio; Conejero, Vicente; Nuez, Fernando; Blanca, Jose M. // BMC Bioinformatics;2008, Vol. 9, Special section p1 

    Background: Expressed sequence tag (EST) collections are composed of a high number of single-pass, redundant, partial sequences, which need to be processed, clustered, and annotated to remove low-quality and vector regions, eliminate redundancy and sequencing errors, and provide biologically...

  • Exploring Parasite Gene Space. Wasmuth, James; Schmid, Ralf; Anthony, Alasdair; Parkinson, John; Blaxter, Mark // BMC Bioinformatics;2005 Supplement 3, Vol. 6, pP27 

    A conference paper on parasite gene space is presented. It describes the investigation of genomes through generation of expressed sequence tags (ESTs). There are over 300,000 ESTs for 36 species of parasitic nematode. The species include whipworm and filarial worms. NEMBASE has been constructed....

  • ApiEST‐DB: analyzing clustered EST data of the apicomplexan parasites. Li, Li; Crabtree, Jonathan; Fischer, Steve; Pinney, Deborah; Stoeckert, Christian J.; Sibley, L. David; Roos, David S. // Nucleic Acids Research;Jan2004, Vol. 32 Issue suppl 1, pd326 

    ApiEST‐DB (http://www.cbil.upenn.edu/paradbs‐servlet/) provides integrated access to publicly available EST data from protozoan parasites in the phylum Apicomplexa. The database currently incorporates a total of nearly 100 000 ESTs from several parasite species of clinical and/or...

  • ESTIMA, a tool for EST management in a multi-project environment. Kumar, Charu G.; LeDuc, Richard; Gong, George; Roinishivili, Levan; Lewin, Harris A.; Lei Liu // BMC Bioinformatics;2004, Vol. 5, p176 

    Background: Single-pass, partial sequencing of complementary DNA (cDNA) libraries generates thousands of chromatograms that are processed into high quality expressed sequence tags (ESTs), and then assembled into contigs representative of putative genes. Usually, to be of value, ESTs and contigs...

  • Construction and application of an electronic spatiotemporal expression profile and gene ontology analysis platform based on the EST database of the silkworm, Bombyx mori. Li- Ping Gan; Wen-Yu Zhang; Yan-Shan Niu; Li Xu; Jian Xi; Ming-Ming Ji; Shi-Qing Xu // Journal of Insect Science;2010, Vol. 10, p1 

    The article discusses a study on the construction and application of EST analysis package (apEST) tool based on the Expressed Sequence Tag (EST) database of the silkworm Bombyx mori. It is stated that this tool was programmed for electronic expression, protein annotation and gene ontology...

Share

Other Topics