Wikis > SOPs > VBRC Outreach SOP

VBRC Outreach SOP

The VBRC needs to advertise itself in appropriate places:  

  • Public web sites/wikis, blogs, blog comments, forums are all opportunities to informally advertise  the VBRC main site and the tools. 
  • Answering posts on forums, or commenting on blogs with info about the site are quick ways to make the VBRC known to researchers.
  • Places we advertise need to be tracked so that the info is current.

 Below is info on:

What to put on sites:

  • Browse the website and find the section most appropriate for  each tool (and/or the VBRC).  There may be more than one; advertise in all relevant sections.
  • Use the summaries provided below.  If necessary, modify the summaries to the appropriate length and/or format.
  • For websites which require the user to set up an account with a username and password, refer to the SOP under the Apollo server: Lab Data/Curation Data/SOPs/VBRC Advertisement SOP.doc
  • After the summaries are visible on the website, copy the exact address for the page(s) of the website on which each of the tools (and/or the VBRC) is advertised.  These addresses should then be added to the the bottom of this page.

Example summaries that can be modified or copied/pasted as is into a textbox that can handle HTML formatting. For other textboxes, you will need to remove the PubMed links – they are in the format: “<pubmed argument…</pubmed>”. You may also need to either remove or change the format of the website link as well.  These are found in the first line of the summaries and are in the format: “[http://www… xxx]” (where xxx is the name of the tool or website to which the preceeding internet address corresponds). 

ORIGINAL CONTENT OF THIS PAGE This page was changed to make things easier, but the original page is here.

The Main Site/VBRC
Viral Bioinformatics Canada: VBRC-University of Victoria is an online resource providing access to curated viral genomes and a variety of tools for comparative genomic analyses.  The resource includes tools such as:

VOCs
 
JDotter
 
Base-by-Base
 
VGO
 
GraphDNA
 
JIPS
 
ReHAB
 
Hydrophobicity Grapher
 

The curated database (containing Adeno-, Arena-, Asfar-, Baculo-, Bunya-, Corona-, Filo-, Flavi-, Herpes-, Irido-, Paramyxo-, Pox- and Togaviridae) is the source of information for other programs of the workbench used for whole genome alignments, genome display or gene/protein sequence analysis.  Many of these tools can also be used with manually-inputted sequence data. The workbench tools are Java-based to allow all users, regardless of computer skill-level, to access and analyze the data.

JDotter
JDotter is a platform-independent Java interactive user interface for the Linux version of Dotter – a widely used program for generating dot plots of DNA or protein sequences which is available at the Dotter homepage.  JDotter runs as a client-server application; JDotter can send new sequences to the Dotter program for alignment as well as rapidly access a repository of pre-processed dot plots. JDotter also interfaces with a sequence database or file system to display supplementary feature data. JDotter, therefore, greatly simplifies access to dot plot data and is especially useful in laboratories that deal with large numbers of genomes and/or have a multi-platform organization.

VOCs
Virus Orthologous Clusters (VOCs) is a java-based user interface that provides access to the genome databases available at virology.ca (Adeno-, Arena-, Asfar-, Baculo-, Bunya-, Corona-, Filo-, Flavi-, Herpes-, Irido-, Paramyxo-, Pox- and Togaviridae). New databases can be built using VOCs and existing databases can be searched to find specific genomes, ortholog groups, genes, proteins and several other associated features.  These results can then be visualized, saved and/or analyzed using a set of tools (many of which can be accessed directly from VOCs).  These tools can be used to create multiple alignments, dot plots, hydrophobicity graphs, DNA graphs, display codon statistics, conduct genome-based fingerprint peptide scanning, compare expected vs. actual frequencies of short nucleotide fragments, filter the results further etc.  VOCs facilitates thorough analysis of genomic data and is a powerful bioinformatics resource.

VGO
Viral Genome Organizer (VGO) is a java based interface used for viewing and searching viral genome sequences. This organizer displays information relevant to a genome of interest, including its genes, ORFs and start/stop codons and can be used to perform a regular expression search, a fuzzy motif search, and a masslist search.  VGO can be used to identify related genes across multiple sequences.

ReHAB
Recent Hits Acquired from BLAST (ReHAB) is a tool used to find new protein hits in repeated PSI-BLAST searches. ReHAB compares results from PSI-BLAST searches performed with two versions of a protein sequence database and highlights hits that are present only in the updated database. Results are presented in tabular format or in the form of a BLAST-like report, using colors to highlight the new hits. ReHAB is designed to handle large numbers of query sequences, such as whole genomes or sets of genomes. As sequence databases continue to grow exponentially, it becomes increasingly important to repeat searches at frequent intervals, and similarity searches retrieve larger and larger sets of results; this software greatly simplifies the problem of evaluating the output of large numbers of protein database searches.

GraphDNA


GraphDNA allows the user to generate graphical representations of raw DNA sequences. Currently there are 8 graphing options and it is possible to plot any of the individal genes or genomes in any format.

Hydrophobicity Grapher
Hydrophobicity Grapher graphs the hydrophobicity/hydrophilicity of a sequence of amino acids using a sliding window. The window size can be specified and several hydrophobicity scales can be used to determine the plot.

JFreq
Java Word Frequencies (JFreq) is a front end to Schbath’s R’MES which is available at the R’MES website.  This is used to find the expected and actual frequencies of short nucleotide sequence strings using a Markov model to account for the effects of base composition and the frequencies of shorter strings. Unusually frequent or infrequent occurrences of certain strings may be indicative of biological relevance. R’MES can also determine whether strings occur in overlapping positions unusually often or unusually rarely frequencies.

GFS java GUI
Genome-based fingerprint scanning Java User Interface (GFS java user interface) is a java interface for GFS which is available at the GFS website.  GFS is a program used to map peptide mass fingerprint (PMF) data directly to raw genomic sequences; this enables the rapid, low-cost identification of potential proteins in unannotated genome sequences.  To scan a genome sequence of interest, an experimentally-obtained PMF is entered into the program the program will then generate a theoretical mass list by translating the genome of interest in 6 reading frames.  This version of GFS should only be used with viral genomes (or similarly-sized DNA sequences).

GATU
Genome Annotation Transfer Utility (GATU) is a platform-independent (java-based) tool designed to efficiently annotate genomes based on a closely related reference genome that is already annotated. Unlike some other annotation tools, GATU does not require sequences to be aligned prior to file import. The program uses BLASTn and tBLASTn algorithms to map genes from the reference genome onto the new sequence. In addition, a NEEDLE alignment of the protein sequences is performed; similarity at both the nucleotide and amino acid level is considered. ORFs present in the target genome and absent from the reference genome are also identified, these can be further analyzed (using BLAST, VGO, BBB etc.) and then accepted or rejected for annotation. GATU can handle multiple-exon genes as well as mature peptides. The goal is to annotate the majority of the new genome’s genes in a single run, making GATU ideal for large sequences. Although it was designed for use with large viral genomes, GATU can also be used to aid in the annotation of larger genomes (such as bacterial genomes). Files can be uploaded in FASTA or GenBank format.

Base-By-Base
Base-By-Base (BBB) is a platform-independent (java-based), whole-genome pairwise and multiple alignment editor. The program highlights differences between pairs of alignments and allows users to easily navigate large alignments of sequences. Although Base-By-Base was intended as an editor and viewer for alignments of highly similar sequences, it also generates multiple alignments using ClustalW, T-Coffee and MUSCLE. It can also be used for annotating genomes with comments or primer sequences.

Sites targeted:

These links should be visited periodically to ensure they are up-to-date and functional.

NB  mybio.net may be dead  (May 6th, 2008).

Places we should maintain a presence:

  • www.bioinformaticsworldwide.com
  • www.openhelix.com/blog/
  • microbiologybytes.wordpress.com
 

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