virology blog
About viruses and viral disease
On episode #358 of the science show This Week in Virology, Vincent meets up with Ileana at Princeton University to talk about how her laboratory integrates molecular virology, mass spectrometry-based proteomics, and bioinformatics to unravel the interplay between virus and host.
You can find TWiV #358 at www.microbe.tv/twiv.
from Brian Foley:
18th International BioInformatics Workshop on Virus Evolution and Molecular Epidemiology
University of Florida, Emerging Pathogens Institute
Gainesville, Florida, USA
August 25th – August 30th, 2013
Bioinformatics Methods Applied to Virology and Epidemiology
Announcing the organization of the international workshop on Virus Evolution and Molecular Epidemiology (VEME) in 2013, hosted by the Emerging Pathogens Institute in the warm city of Gainesville and sponsored by several local partners.
We plan to organize a ‘Phylogenetic Inference’ module that offers the theoretical background and hands-on experience in phylogenetic analysis for those who have little or no prior expertise in sequence analysis. An ‘Evolutionary Hypothesis Testing’ is targeted to participants who are well familiar with alignments and phylogenetic trees, and would like to extend their expertise to likelihood and Bayesian inference in phylogenetics, coalescent and phylogeographic analyses (‘phylodynamics’) and molecular adaptation. A ‘Large Dataset Analysis’ module will cover the more complex analysis of full genomes, huge datasets of pathogens including Next Generation Sequencing data, and combined analyses of pathogen and host. Practical sessions in these modules will involve software like, PHYLIP, PAUP*, PHYML, MEGA, PAML or HYPHY, TREE-PUZZLE, SplitsTree, BEAST, MrBayes Simplot and RDP3.
We recommend participants to buy The Phylogenetic Handbook as a guide during the workshop, and to bring their own data set.
For further information and applications check this website.
Abstract and application deadline is April 30th.
Selections will be made by end of May 2013.
The registration fee of 1000 USD covers attendance, lunches and coffee breaks.
Participation is limited to 25 scientists in each module and is dependent on a selection procedure based on the submitted abstract and statement of motivation. A limited number of grants are available for scientists who experience difficulties to attend because of financial reasons.
On episode #192 of the science show This Week in Virology, Vincent, Alan, and Rich answer listener email about bioinformatics, insects, influenza, laboratory classes, commensalism, reproducibility of data, and more.
You can find TWiV #192 at www.microbe.tv/twiv.
This week’s addition to the virology toolbox was written by Chris Upton
Sequence Searcher is a Java program that allows users to search for specific sequence motifs in protein or DNA sequences. For example, it can be used to identify restriction enzyme cleavage sites or find similar sequence patterns among multiple sequences. Most searches run in a few seconds.
Sequence Searcher is part of the Virology.ca suite of programs available at the University of Victoria.
Help files:
Some of the key features of Sequence Searcher include:
For DNA, the searches are conducted by finding the motif within a sequence from the 5’ to 3’ end on the top strand. The searches are also processed from the 5’ to 3’ end of the bottom strand. As a result, bases are numbered from 1 starting at the 5’ at either the top or bottom strand.
Regular expression and fuzzy pattern searches are available:
Fuzzy searches provide the option for the program to allow a certain number of mismatches from a sequence input at any position. Note that the maximum number of mismatches that the program allows is 40% of the length of the sequence motif.
Regular expression allows for inputs of precise motifs along with considerable user-specified flexibility at specific positions.
Figure 1. The input tab is where you can import DNA or protein sequences (must be in FASTA format) and type in the specific pattern to search within in the sequence(s). The search type can be selected as “Regular expression†or “Fuzzy†by using the drop down menu.
Figure 2. When a search has been completed, the results tab is presented in a table format. The results in the table can be sorted depending on the column header (sequence, match, start, stop, confidence, and strand). The results can also be filtered by sequence and strand by selecting the drop down menus at the top.
Marass, F., & Upton, C. (2009). Sequence Searcher: A Java tool to perform regular expression and fuzzy searches of multiple DNA and protein sequences BMC Research Notes, 2 (1) DOI: 10.1186/1756-0500-2-14
This week’s addition to the virology toolbox was written by Chris Upton (Disclaimer: BBB was developed in the Upton lab, so this is a biased review.)
This will be a multi-part posting describing the key features of BBB.
Base-By-Base (BBB) is a Java (platform independent) multiple sequence alignment (MSA) editor. Development was begun many years ago to provide a virologist-friendly tool to work with MSAs of proteins, gene sequences and also genome sequences (up to about 500 kb). Over the years we have added many unique features, as they have been needed by our own research with a variety of virus genomes; development has been driven by the users – who spend a lot of their day looking at a variety of MSAs!
BBB is available here.
The program is Open Source and freely available to all academic labs.
Help files:
Key features:
Figure 1A. Differences between sequences are high-lighted. Blue=nt substitution; Green=nt deletion; Red=nt insertion.
Figure 1B. Edited version of Figure 1A (my opinion).
Figure 1C. Same alignment as 1B, but differences are set for compare against top sequence.
Figure 1D. Same alignment and differences setting, but Sequence-2 has been moved to the bottom of the alignment (use arrows on left edge of window).
Figure 2A. Two sequences have been hidden. 3-frame translation is shown. Top strand is shown by default.
Figure 2B. Switched to bottom strand display (use top right button; 5’Top3’ in Fig. 2A). Notice direction of arrows in aa translation.
Figure 3. Gene annotations from GenBank file (pink); mouse-over gives gene annotation (#083) and nucleotide position. User-added comments: Blue=comment on Top stand; comments associated with strand not currently displayed are shown as outlines.
Figure 4A. Editing a sequence. First, select a region.
Figure 4B. Editing a sequence. Second, delete the selection.
Figure 4C. Editing a sequence. Third, add new nucleotides.
Tips:
This week’s addition to the virology toolbox was written by Chris Upton
The Jalview package: a multiple alignment editor.
This software is primarily aimed at the alignment of protein sequences. Some of the key features are:
Tips:
If you use Jalview in your work, you should cite the Jalview 2 publication:
• Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M., Barton, G.J (2009), Jalview version 2: A Multiple Sequence Alignment and Analysis Workbench. Bioinformatics 25:1189-91.
• Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor. Bioinformatics 20: 426-7.