WEB-BASED BIOINFORMATICS SEVICES
We have developed the Bioportal bioinformatics service at University of Oslo. The service was the most used web-based bioinformatics service in Norway with users from most life science research environments in Norway and hundreds of users from other countries. More than 5000 users were registered from Norway and other countries. Core members of the project team was composed of persons employed at USIT and Department of Biology (both UiO). The Bioportal was supported as a technology platform by the Molecular Life Science Board at University of Oslo.
Please refer to the following article if you have used Bioportal:
Surendra Kumar, Åsmund Skjæveland, Russell JS Orr, Pål Enger, Torgeir Ruden, Bjørn-Helge Mevik, Fabien Burki, Andreas Botnen and Kamran Shalchian-Tabrizi. AIR: A batch-oriented web program package for construction of supermatrices ready for phylogenomic analyses. BMC Bioinformatics 2009, 10:357 doi:10.1186/1471-2105-10-357.
Lifeportal - a new web-based portal
The Bioportal has been replaced by Lifeportal. If you need a reference to Lifeportal, you may want to use: Kumar Surendra Kumar, Anders K. Krabberød, Ralf S. Neumann, Katerina Michalickova, Sen Zhao, Xiaoli Zhang and Kamran Shalchian-Tabrizi. BIR Pipeline for Preparation of Phylogenomic Data. Evolutionary Bioinformatics 2015. In press.
COMPUTER PROGRAMS AND PIPELINES
The BLASTGrabber application introduces new ways of visualizing and analysing massive BLAST output data by integrating taxonomy identification, text mining capabilities and generic multi-dimensional rendering of BLAST hits. The program aims at a non-expert audience in terms of computer skills; the combination of new functionalities makes the program flexible and useful for a broad range of operations.
The AIR pipeline develops multi gene alignments. It enables calculation of evolutionary rates of sites in multiple sequence alignments. Removing fast evolving sites with the AIR programs has been employed in several recent phylogenomic analyses resulting in improved phylogenetic resolution and increased statistical support for branching patterns among the early diverging eukaryotes.
BIR (Blast, Identify and Realign) identify gene sequences applicable for phylogenomic inference. The pipeline allows users to apply their own manually curated sequence alignments (seed) in search for homologous genes in sequence databases and available genomes. BIR automatically adds the identified sequences from these databases to the seed alignments and reconstruct a phylogenetic tree from each. The BIR pipeline is an efficient tool for the identification of orthologous gene copies because it expands user-defined sequence alignments and conducts massive parallel phylogenetic reconstruction. The application is also particularly useful for large-scale sequencing projects that require management of a large number of single-gene alignments for gene comparison, functional annotation, and evolution-ary analyses.
Accepted in Evolutionary Bioinformatics
The implementation of high throughput sequencing for exploring biodiversity poses high demands on bioinformatics applications for automated data processing. Here we introduce CLOTU, an online and open access pipeline for processing 454 amplicon reads. CLOTU has been constructed to be highly user-friendly and flexible, since different types of analyses are needed for different datasets. CLOTU is a flexible and easy to use bioinformatics pipeline that includes different options for filtering, trimming, clustering and taxonomic annotation of high throughput sequence reads. Some of these options are not included in comparable pipelines. The pipeline is available on Lifeportal.
Review article on BLAST output analyses - in Briefings in Bioinformatics
The Basic Local Alignment Search Tool (BLAST) algorithm remains one of the most widely used bioinformatic programs. For many projects, new sequencing technologies and increased database sizes will increase the BLAST output significantly. Frequently, this output is so large that it is no longer able to be processed manually. As BLAST users are increasingly recruited from mainstream biology without any bioinformatic background, user-friendly programs capable of BLAST output visualization, analysis and post-processing are in demand. In this review, freely available BLAST output processing programs are categorized as BLAST output interpreters, BLAST environments, BLAST output parsers or specialized tools. They are evaluated according to their user-friendliness, analysis features and high-throughput data processing capabilities.