November 2012

Virus Pathogen Resource (ViPR) New Features in ViPR

genome sequences with incomplete CDS. tool to allow primer design for a group of target News and Events Currently, the annotation pipeline has been sequences in the future . implemented to predict mature viral proteins for In response to user feedback, we have also added Join the ViPR User Advisory many taxa in the Arenaviridae , Bunyaviridae , end-of-line position numbers in the primer design Group to help us better serve Caliciviridae , Coronaviridae , Flaviviridae , and sequence input sequence box. This feature will the scientific community Togaviridae families in ViPR . help ensure accurate selection of the desired ViPR is a bioinformatics resources built for the target region within the displayed sequence. virology research community. We are calling for users to join the ViPR User Advisory Group to provide feedback and advise on ViPR Rock your development. Click here for details . protein structure IRD/ViPR hands-on workshops ViPR provides a ViPR will be providing a hands-on workshop customized at Mount Sinai School of Medicine, New interactive York, NY, December 5 . Please contact Ryan protein Camping ( [email protected] ) for structure workshop registration. viewer for virus-related protein structures obtained from the Protein Data Bank . In addition to PCR primer design tool enhanced choosing from a variety of structure display Sequence Conservation/ ViPR has recently implemented a PCR primer options , including ball & stick, line, space, primary Variation Analysis tutorial design tool , which uses the Primer3 algorithm to The Analyze Sequence Variation (SNP) tool in structure, secondary structure, etc., you can now predict the optimal set(s) of PCR primers for a ViPR provides the ability to quickly quantify rock a structure back and forth to get a better 3D particular sequence . In addition to uploading or the sequence variations present at all view of your region of interest. First orient or zoom homologous positions for user-selected the structure to your needs, then click the “Rock ” sequences at either the nucleotide or amino button in the Display Options section and adjust acid level and simultaneously calculates the the rocking parameters if needed . Take a look at a consensus sequence . Check out the tutorial to sample structure here . see how to use it.

Improved mature viral protein annotation pipeline In addition to integrating virus -related data from pasting your own nucleotide sequence to the PCR multiple public repositories, the ViPR Primer Design tool page accessible from the Bioinformatics Resource Center has also “Analyze & Visualize ” tab , you can now launch developed a variety of custom annotation and the PCR Primer Design tool directly from either a computational pipelines . E:orts to improve Nucleotide Search Results page or from a Working protein annotations by the ViPR team are Set Details page within your personalized exempli;ed in the recent development of a n Workbench. To do so, on the Search Results page Added support for Rhabdoviridae annotation pipeline designed to predict regions or Working Set Details page, select the desired viruses containing mature viral proteins from polyprotein sequence, mouse over the“ Run Analysis ” menu In addition to supporting the Lyssavirus genus in sequence data obtained from GenBank. This and click“ PCR Primer Design ”. Your selected the Rhabdoviridae family , ViPR has added pipeline combines multiple sequence alignment sequence will automatically be transferred to the sequence, immune epitope, and protein structure with protease cleavage site information from PCR Primer Design tool. At present, primers can data for Bracorhabdovirus , Cytorhabdovirus, well-annotated Reference Sequence (RefSeq ) only be designed for one target sequence at a Ephemerovirus, Novirhabdovirus , strains for each virus taxon, to map the time . However, ViPR is working on enhancing the Nucleorhabdovirus , Vesiculovirus (Vesicular homologous mature peptide locations from the Stomatitis Virus), and unclassi;ed Rhabdoviridae RefSeq record to the other genome sequences viruses (Bas-Congo virus ) in Rhabdoviridae . Come within the same virus taxon . This pipeline was The November 2012 release of to ViPR to search for the various types of data recently improved by incorporating the ClustalW ViPR is now available, visit integrated in the database and take advantage of algorithm for the multiple sequence alignment the suite of analysis and visualization tools step in order to improve accuracy, especially for www.viprbrc.org/brc/ provided in ViPR.

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