Virology and Bioinformatics from Virology.ca
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Virology and Bioinformatics from Virology.ca
Virus and bioinformatics articles with some microbiology and immunology thrown in for good measure
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FastaHerder2: Four Ways to Research Protein Function and Evolution with Clustering and Clustered Databases | Abstract

"The accelerated growth of protein databases offers great possibilities for the study of protein function using sequence similarity and conservation. However, the huge number of sequences deposited in these databases requires new ways of analyzing and organizing the data. It is necessary to group the many very similar sequences, creating clusters with automated derived annotations useful to understand their function, evolution, and level of experimental evidence. We developed an algorithm called FastaHerder2, which can cluster any protein database, putting together very similar protein sequences based on near-full-length similarity and/or high threshold of sequence identity. We compressed 50 reference proteomes, along with the SwissProt database, which we could compress by 74.7%. The clustering algorithm was benchmarked using OrthoBench and compared with FASTA HERDER, a previous version of the algorithm, showing that FastaHerder2 can cluster a set of proteins yielding a high compression, with a lower error rate than its predecessor. We illustrate the use of FastaHerder2 to detect biologically relevant functional features in protein families. With our approach we seek to promote a modern view and usage of the protein sequence databases more appropriate to the postgenomic era."

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BMC Genomics | Abstract | HTRIdb: an open-access database for experimentally verified human transcriptional regulation interactions

The HTRIdb is implemented as a relational database PostgreSQL that is connected to a web interface via the JBOSS AS that dynamically generates user-friendly HTML front-end queries using the Apache Tomcat web server. For the network visualization of interactions, HTRIdb uses the web version of the popular Cytoscape visualization tool (Cytoscape Web). The TF-TG interactions data currently present in HTRIdb have been collected from original research articles.

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Sequence database versioning for command line and Galaxy bioinformatics servers. - PubMed - NCBI

There are various reasons for rerunning bioinformatics tools and pipelines on sequencing data, including reproducing a past result, validation of a new tool or workflow using a known dataset, or tracking the impact of database changes. For identical results to be achieved, regularly updated reference sequence databases must be versioned and archived.
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HIVdb Mutation Input

Protease, RT, and integrase mutations can be entered using either the text box or pull down menus.

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