Biomedical subjects

Karsten Hokamp

Publications and source records attributed to Karsten Hokamp.

7 recordsLinked to original sources

PubMed2004

ArrayPipe: a flexible processing pipeline for microarray data.

A number of microarray analysis software packages exist already; however, none combines the user-friendly features of a web-based interface with potential ability to analyse multiple arrays at once using flexible analysis steps. The ArrayPipe web server (freely available at www.pathogenomics.ca/arraypipe) allows the automated application of complex analyses to microarray data which can range from single slides to large data sets including replicates and dye-swaps. It handles output from most commonly used quantification software packages for dual-labelled arrays. Application features range from quality assessment of slides through various data visualizations to multi-step analyses including normalization, detection of differentially expressed genes, andcomparison and highlighting of gene lists. A highly customizable action set-up facilitates unrestricted arrangement of functions, which can be stored as action profiles. A unique combination of web-based and command-line functionality enables comfortable configuration of processes that can be repeatedly applied to large data sets in high throughput. The output consists of reports formatted as standard web pages and tab-delimited lists of calculated values that can be inserted into other analysis programs. Additional features, such as web-based spreadsheet functionality, auto-parallelization and password protection make this a powerful tool in microarray research for individuals and large groups alike.

Gene Expression Profiling↗

PubMed2004

ProbeLynx: a tool for updating the association of microarray probes to genes.

As genome sequence data and gene prediction improve, probes developed for a given microarray experiment should be continuously re-evaluated for their specificity for given genes. ProbeLynx(www.pathogenomics.ca/probelynx) is a new web service which uses current genomic sequence information to re-examine microarray probe specificity and provide annotation updates relevant to determining which gene(s) and transcript(s) are associated with a given probe. Probe sequences (either oligonucleotide- or cDNA-based) are uploaded in FASTA format and the results returned as a tab-delimited flat file for insertion into a spreadsheet application or database management system for further analysis. ProbeLynx has been initially developed to focus on arrays derived from human, mouse, chicken and bovine genomes, but may be expanded to handle other genomic datasets. ProbeLynx offers microarray users the important ability to continuously assess the potential of a probe to cross-hybridize to paralogous genes and the suitability of a given probe to investigate a transcript of interest. By also including the latest gene function annotation information in the output, ProbeLynx provides the critical first step in updating microarray data annotation.

Animals↗

PubMed2004

PubCrawler: keeping up comfortably with PubMed and GenBank.

The free PubCrawler web service (http://www.pubcrawler.ie) has been operating for five years and so far has brought literature and sequence updates to over 22 000 users. It provides information on a personalized web page whenever new articles appear in PubMed or when new sequences are found in GenBank that are specific to customized queries. The server also acts as an automatic alerting system by sending out short notifications or emails with the latest updates as soon as they become available. A new output format and more flexibility for the email formatting help PubCrawler cope with increasing challenges arising from browser incompatibilities and mail filters, therefore making it suitable for a wide range of users.

Databases, Nucleic Acid↗

PubMed2003

Wrapping up BLAST and other applications for use on Unix clusters.

UNLABELLED: We have developed two programs that speed up common bioinformatic applications by spreading them across a UNIX cluster.(1) BLAST.pm, a new module for the 'MOLLUSC' package. (2) WRAPID, a simple tool for parallelizing large numbers of small instances of programs such as BLAST, FASTA and CLUSTALW. AVAILABILITY: The packages were developed in Perl on a 20-node Linux cluster and are provided together with a configuration script and documentation. They can be freely downloaded from http://wolfe.gen.tcd.ie/wrapper.

Computer Communication Networks↗

PubMed2003

A recent polyploidy superimposed on older large-scale duplications in the Arabidopsis genome.

The Arabidopsis genome contains numerous large duplicated chromosomal segments, but the different approaches used in previous analyses led to different interpretations regarding the number and timing of ancestral large-scale duplication events. Here, using more appropriate methodology and a more recent version of the genome sequence annotation, we investigate the scale and timing of segmental duplications in Arabidopsis. We used protein sequence similarity searches to detect duplicated blocks in the genome, used the level of synonymous substitution between duplicated genes to estimate the relative ages of the blocks containing them, and analyzed the degree of overlap between adjacent duplicated blocks. We conclude that the Arabidopsis lineage underwent at least two distinct episodes of duplication. One was a polyploidy that occurred much more recently than estimated previously, before the Arabidopsis/Brassica rapa split and probably during the early emergence of the crucifer family (24-40 Mya). An older set of duplicated blocks was formed after the monocot/dicot divergence, and the relatively low level of overlap among these blocks indicates that at least some of them are remnants of a larger duplication such as a polyploidy or aneuploidy.

Arabidopsis↗

PubMed2003

The 2R hypothesis and the human genome sequence.

One theory formalised in 1970 proposes that the complexity of vertebrate genomes originated by means of genome duplication at the base of the vertebrate lineage. Since then, the theory has remained both popular and controversial. Here we review the theory, and present preliminary results from our analysis of duplications in the draft human genome sequence. We find evidence for extensive duplication of parts of the genome. We also question the validity of the 'parsimony test' that has been used in other analyses.

Animals↗

PubMed2002

Extensive genomic duplication during early chordate evolution.

Opinions on the hypothesis that ancient genome duplications contributed to the vertebrate genome range from strong skepticism to strong credence. Previous studies concentrated on small numbers of gene families or chromosomal regions that might not have been representative of the whole genome, or used subjective methods to identify paralogous genes and regions. Here we report a systematic and objective analysis of the draft human genome sequence to identify paralogous chromosomal regions (paralogons) formed during chordate evolution and to estimate the ages of duplicate genes. We found that the human genome contains many more paralogons than would be expected by chance. Molecular clock analysis of all protein families in humans that have orthologs in the fly and nematode indicated that a burst of gene duplication activity took place in the period 350 650 Myr ago and that many of the duplicate genes formed at this time are located within paralogons. Our results support the contention that many of the gene families in vertebrates were formed or expanded by large-scale DNA duplications in an early chordate. Considering the incompleteness of the sequence data and the antiquity of the event, the results are compatible with at least one round of polyploidy.

Animals↗