Viral Bioinformatics Resource Center - Other Tools Provided By VBRC

Other Tools Provided By VBRC

VBRC provides a number of additional Java-based analysis tools on its website. Several are interfaces to pre-existing bioinformatics tools (e.g. napC, R’MES), while others were independently developed by VBRC. The tools in this category are each designed to perform a very specific task (e.g. regular expression searches, DNA skew plotting) and, though they can be accessed as stand-alone programs with user-supplied input, most have increased utility when launched from the central VOCS application with VBRC-supplied data.

These additional tools are as follows:

• Sequence Searcher performs regular expression and fuzzy motif searches of DNA or protein sequences, and is built into VOCS.
• GFS (Genome Fingerprint Scanning) maps peptide mass fingerprint data to genomic sequences. It is built into VOCS.
• NAP (Nucleotide Amino Acid Alignment) is a Java interface to napC, a program designed to align a nucleotide and protein sequence, taking terminal gaps and insertion/deletion mutations into account. It can be accessed from VOCS.
• GraphDNA provides DNA skews and walks (a Cartesian plane-based representation of nucleotide content) from a VBRC database- or user-supplied DNA sequence. It is integrated into VOCS.
• Hydrophobicity Plotter generates a hydrophobicity graph for a VBRC database- or user-supplied protein sequence. Three hydrophobicity scales (Kyte-Doolittle, Hopp-Woods, and Parker-Guo-Hodges) are supported; the graphing procedure is based on a sliding window of user-determined length. It can be accessed from VOCS.
• CS (Codon Statistics) allows the user to generate statistical data and graphical representations of the nucleotide content of a VBRC database- or user-supplied DNA sequence (generally an entire genome).
• JFreq (Java Word Frequencies) is a Java interface to the R’MES program, which allows the user to find and statistically analyze unusual frequencies or distributions of words (short sequence patterns) within a DNA sequence.
• GATU (Genome Annotation Transfer Utility) allows a user to annotate a newly sequenced genome based on the annotations present in a reference genome; it can also predict new genes in the query genome.
• REHAB (Recent Hits Acquired from BLAST) is a stand-alone program allowing the bioinformatics researcher to store and compare information obtained by successive PSI-BLAST runs of a single sequence against the continually updated NCBI Genbank database.
• JIPS (Java GUI for InterProScan) is similar to REHAB in that it allows the user to identify new results (motifs, fingerprints, or domains) in successive searches of a protein sequence against the InterProScan database.

The VBRC also provides a number of Web-based, rather than downloadable, analysis tools on its site, including:

• A Genome List and Ortholog Comparison tool, giving Web-based text and/or graphical access to much of the data supplied by VOCS (see above).
• An XS-Blast tool allowing the researcher to form a private SQL database for storing, retrieving, and filtering the XML results of repeated BLAST searches for a particular query sequence.
• A separate Hepatitis C (HCV) Database providing bioinformatic and immunological data. This represents a consortium between VBRC, the Immune Epitope Database and Analysis Resource (IEDB), and the Hepatitis C Virus Resource at the Los Alamos National Laboratory (HCV-LANL).
• A separate Dengue Database providing bioinformatic, immunological, and epidemiological data. This represents a consortium between VBRC, the Immune Epitope Database and Analysis Resource (IEDB), and the Broad Institute Microbial Sequencing Center (MSC).
• A Knowledge Database containing curated genes and graphical gene maps for several reference genomes selected from the Ebolaviridae, Flaviviridae, and Poxviridae families. Information presented includes functional, structural, and gene expression data, together with relevant references.