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OrchidBase: A collection of sequences of transcriptome derived from orchids.
Plant Cell Physiol. 2011 Jan 17;
Authors: Fu CH, Chen YW, Hsiao YY, Pan ZJ, Liu ZJ, Huang YM, Tsai WC, Chen HH
Orchids are one of the most ecological and evolutionary significant plants, and the Orchidaceae is one of the most abundant families in angiosperm. The genetic databases will be useful not only for gene discovery but future genomic annotation. For this purpose, OrchidBase was established from 37,979,342 sequence reads collected from eleven in-house Phalaenopsis orchid cDNA libraries. Among them, 41,310 expressed sequence tags (ESTs) were obtained by using Sanger sequencing, whereas 37,908,032 reads were obtained by using next generation sequencing (NGS) including both Roche 454 and Solexa Illumina sequencers. These reads were assembled into 8,501 contigs and 76,116 singletons, resulting 84,617 non-redundant transcribed sequences with an average length of 459 bp. The analysis pipeline of database is an automated system written in Perl and C#, and consists of the following components: automatic preprocessing of EST reads, assembly of raw sequences, annotation of the assembled sequences, and storage of the analyzed information into SQL databases. A web application was implemented with HTML and Microsoft .NET Framework C# program for browsing and querying the database, creating of dynamic web pages on the client side, analyzing Gene Ontology (GO), and for mapping annotated enzymes to KEGG pathways. The online resources for putative annotation can be searched either by text or by using BLAST, and the results can be explored on the website and downloaded. Consequently, the establishment of OrchidBase will provide researchers a high-quality genetic resource for data-mining and facilitate efficient experimental studies on orchid biology and biotechnology. The OrchidBase database is freely available at http://lab.fhes.tn.edu.tw/est.
PMID: 21245031 [PubMed - as supplied by publisher]
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OrchidBase: A collection of sequences of transcriptome derived from orchids.
Plant Cell Physiol. 2011 Jan 17;
Authors: Fu CH, Chen YW, Hsiao YY, Pan ZJ, Liu ZJ, Huang YM, Tsai WC, Chen HH
Orchids are one of the most ecological and evolutionary significant plants, and the Orchidaceae is one of the most abundant families in angiosperm. The genetic databases will be useful not only for gene discovery but future genomic annotation. For this purpose, OrchidBase was established from 37,979,342 sequence reads collected from eleven in-house Phalaenopsis orchid cDNA libraries. Among them, 41,310 expressed sequence tags (ESTs) were obtained by using Sanger sequencing, whereas 37,908,032 reads were obtained by using next generation sequencing (NGS) including both Roche 454 and Solexa Illumina sequencers. These reads were assembled into 8,501 contigs and 76,116 singletons, resulting 84,617 non-redundant transcribed sequences with an average length of 459 bp. The analysis pipeline of database is an automated system written in Perl and C#, and consists of the following components: automatic preprocessing of EST reads, assembly of raw sequences, annotation of the assembled sequences, and storage of the analyzed information into SQL databases. A web application was implemented with HTML and Microsoft .NET Framework C# program for browsing and querying the database, creating of dynamic web pages on the client side, analyzing Gene Ontology (GO), and for mapping annotated enzymes to KEGG pathways. The online resources for putative annotation can be searched either by text or by using BLAST, and the results can be explored on the website and downloaded. Consequently, the establishment of OrchidBase will provide researchers a high-quality genetic resource for data-mining and facilitate efficient experimental studies on orchid biology and biotechnology. The OrchidBase database is freely available at http://lab.fhes.tn.edu.tw/est.
PMID: 21245031 [PubMed - as supplied by publisher]
More...