Biomedical subjects

Eileen Kraemer

Publications and source records attributed to Eileen Kraemer.

5 recordsLinked to original sources

PubMed2006

ApiDB: integrated resources for the apicomplexan bioinformatics resource center.

ApiDB (http://ApiDB.org) represents a unified entry point for the NIH-funded Apicomplexan Bioinformatics Resource Center (BRC) that integrates numerous database resources and multiple data types. The phylum Apicomplexa comprises numerous veterinary and medically important parasitic protozoa including human pathogenic species of the genera Cryptosporidium, Plasmodium and Toxoplasma. ApiDB serves not only as a database in its own right, but as a single web-based point of entry that unifies access to three major existing individual organism databases (PlasmoDB.org, ToxoDB.org and CryptoDB.org), and integrates these databases with data available from additional sources. Through the ApiDB site, users may pose queries and search all available apicomplexan data and tools, or they may visit individual component organism databases.

Animals↗

PubMed2006

CryptoDB: a Cryptosporidium bioinformatics resource update.

The database, CryptoDB (http://CryptoDB.org), is a community bioinformatics resource for the AIDS-related apicomplexan-parasite, Cryptosporidium. CryptoDB integrates whole genome sequence and annotation with expressed sequence tag and genome survey sequence data and provides supplemental bioinformatics analyses and data-mining tools. A simple, yet comprehensive web interface is available for mining and visualizing the data. CryptoDB is allied with the databases PlasmoDB and ToxoDB via ApiDB, an NIH/NIAID-fundedBioinformatics Resource Center. Recent updates to CryptoDB include the deposition of annotated genome sequences for Cryptosporidium parvum and Cryptosporidium hominis, migration to a relational database (GUS), a new query and visualization interface and the introduction of Web services.

Animals↗

PubMed2004

Calculation, visualization, and manipulation of MASTs (Maximum Agreement Subtrees).

UNLABELLED: Phylogenetic trees are used to represent the evolutionary history of a set of species. Comparison of multiple phylogenetic trees can help researchers find the common classification of a tree group, compare tree construction inferences or obtain distances between trees. We present TreeAnalyzer, a freely available package for phylogenetic tree comparison. A MAST (Maximum Agreement Subtree) algorithm is implemented to compare the trees. Additional features of this software include tree comparison, visualization, manipulation, labeling, and printing. AVAILABILITY: http://www.cs.uga.edu/~eileen/TreeAnalyzer.

Algorithms↗

PubMed2003

GFPE: gene-finding program evaluation.

Gene-finding program evaluation (GFPE) is a set of Java classes for evaluating gene-finding programs. A command-line interface is also provided. Inputs to the program include the sequence data (in FASTA format), annotations of "actual" sequence features, and annotations of "predicted" sequence features. Annotation files are in the General Feature Format promoted by the Sanger center. GFPE calculates a number of metrics of accuracy of predictions at three levels:the coding level, the exon level, and the protein level.

Computational Biology↗

PubMed2003

Mapping by sequencing the Pneumocystis genome using the ordering DNA sequences V3 tool.

A bioinformatics tool called ODS3 has been created for mapping by sequencing. The tool allows the creation of integrated genomic maps from genetic, physical mapping, and sequencing data and permits an integrated genome map to be stored, retrieved, viewed, and queried in a stand-alone capacity, in a client/server relationship with the Fungal Genome Database (FGDB), and as a web-browsing tool for the FGDB. In that ODS3 is programmed in Java, the tool promotes platform independence and supports export of integrated genome-mapping data in the extensible markup language (XML) for data interchange with other genome information systems. The tool ODS3 is used to create an initial integrated genome map of the AIDS-related fungal pathogen, Pneumocystis carinii. Contig dynamics would indicate that this physical map is approximately 50% complete with approximately 200 contigs. A total of 10 putative multigene families were found. Two of these putative families were previously characterized in P. carinii, namely the major surface glycoproteins (MSGs) and HSP70 proteins; three of these putative families (not previously characterized in P. carinii) were found to be similar to families encoding the HSP60 in Schizosaccharomyces pombe, the heat-shock psi protein in S. pombe, and the RNA synthetase family (i.e., MES1) in Saccharomyces cerevisiae. Physical mapping data are consistent with the 16S, 5.8S, and 26S rDNA genes being single copy in P. carinii. No other fungus outside this genus is known to have the rDNA genes in single copy.

Computational Biology↗