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At least 145 records · Page 8Linked to original sources
PubMed2004

WebVar: A resource for the rapid estimation of relative site variability from multiple sequence alignments.

UNLABELLED: WebVar is an online resource that provides estimates of relative site variability from multiple alignments of homologous protein or nucleic acid sequences. WebVar provides a variety of graphic and textual representations of estimates, designed to assist in phylogenetic analysis. AVAILABILITY: The WebVar server is located at http://www.pesolelab.it/Tools/WebVar.html

Algorithms↗
PubMed2005

High-resolution mapping of the barley leaf rust resistance gene Rph5 using barley expressed sequence tags (ESTs) and synteny with rice.

The rapidly growing expressed sequence tag (EST) resources of species representing the Poacea family and availability of comprehensive sequence information for the rice (Oryza sativa) genome create an excellent opportunity for comparative genome analysis. Extensive synteny between rice chromosome 1 and barley (Hordeum vulgare L.) chromosome 3 has proven extremely useful for saturation mapping of chromosomal regions containing target genes of large-genome barley with conserved orthologous genes from the syntenic regions of the rice genome. Rph5 is a gene conferring resistance to the barley leaf rust pathogen Puccinia hordei. It was mapped to chromosome 3HS, which is syntenic with rice chromosome 1S. The objective of this study was to increase marker density within the sub-centimorgan region around Rph5, using sequence-tagged site (STS) markers that were developed based on barley ESTs syntenic to the phage (P1)-derived artificial chromosome (PAC) clones comprising the distal region of rice chromosome 1S. Five rice PAC clones were used as queries in a blastn search to screen 375,187 barley ESTs. Ninety-four non-redundant EST sequences were identified from the EST database and used as templates to design 174 pairs of primer combinations. As a result, 9 barley EST-based STS markers were incorporated into the 'Bowman' x 'Magnif 102' high-resolution map of the Rph5 region. More importantly, six markers, including five EST-derived STS sequences, were found to co-segregate with Rph5. The results of this study demonstrate the usefulness of rice genomic resources for efficient deployment of barley ESTs for marker saturation of targeted barley genomic regions.

Basidiomycota↗
PubMed2003

PlasmoDB: the Plasmodium genome resource. A database integrating experimental and computational data.

PlasmoDB (http://PlasmoDB.org) is the official database of the Plasmodium falciparum genome sequencing consortium. This resource incorporates the recently completed P. falciparum genome sequence and annotation, as well as draft sequence and annotation emerging from other Plasmodium sequencing projects. PlasmoDB currently houses information from five parasite species and provides tools for intra- and inter-species comparisons. Sequence information is integrated with other genomic-scale data emerging from the Plasmodium research community, including gene expression analysis from EST, SAGE and microarray projects and proteomics studies. The relational schema used to build PlasmoDB, GUS (Genomics Unified Schema) employs a highly structured format to accommodate the diverse data types generated by sequence and expression projects. A variety of tools allow researchers to formulate complex, biologically-based, queries of the database. A stand-alone version of the database is also available on CD-ROM (P. falciparum GenePlot), facilitating access to the data in situations where internet access is difficult (e.g. by malaria researchers working in the field). The goal of PlasmoDB is to facilitate utilization of the vast quantities of genomic-scale data produced by the global malaria research community. The software used to develop PlasmoDB has been used to create a second Apicomplexan parasite genome database, ToxoDB (http://ToxoDB.org).

Animals↗
PubMed2006

The Macrostomum lignano EST database as a molecular resource for studying platyhelminth development and phylogeny.

We report the development of an Expressed Sequence Tag (EST) resource for the flatworm Macrostomum lignano. This taxon is of interest due to its basal placement within the flatworms. As such, it provides a useful comparative model for understanding the development of neural and sensory organization. It was anticipated on the basis of previous studies [e.g., Sánchez-Alvarado et al., Development, 129:5659-5665, (2002)] that a wide range of developmental markers would be expressed in later-stage macrostomids, and this proved to be the case, permitting recovery of a range of gene sequences important in development. To this end, an adult Macrostomum cDNA library was generated and 7,680 Macrostomum ESTs were sequenced from the 5' end. In addition, 1,536 of these aforementioned sequences were sequenced from the 3' end. Of the roughly 5,416 non-redundant sequences identified, 68% are similar to previously reported genes of known function. In addition, nearly 100 specific clones were obtained with potential neural and sensory function. From these data, an annotated searchable database of the Macrostomum EST collection has been made available on the web. A major objective was to obtain genes that would allow reconstruction of embryogenesis, and in particular neurogenesis, in a basal platyhelminth. The sequences recovered will serve as probes with which the origin and morphogenesis of lineages and tissues can be followed. To this end, we demonstrate a protocol for combined immunohistochemistry and in situ hybridization labeling in juvenile Macrostomum, employing homologs of lin11/lim1 and six3/optix. Expression of these genes is shown in the context of the neuropile/muscle system.

Animals↗