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The hepatitis C sequence database in Los Alamos.

Kuiken C, Hraber P, Thurmond J, Yusim K - Nucleic Acids Res. (2007)

Bottom Line: The hepatitis C virus (HCV) is a significant public health threat worldwide.Presently, approximately 50 000 HCV sequences have been published.A central website that provides annotated sequences and analysis tools will be helpful to HCV scientists worldwide.

View Article: PubMed Central - PubMed

Affiliation: HCV database, Los Alamos National Laboratory, Los Alamos, NM, USA. kuiken@lanl.gov

ABSTRACT
The hepatitis C virus (HCV) is a significant public health threat worldwide. The virus is highly variable and evolves rapidly, making it an elusive target for the immune system and for vaccine and drug design. Presently, approximately 50 000 HCV sequences have been published. A central website that provides annotated sequences and analysis tools will be helpful to HCV scientists worldwide. The HCV sequence database collects and annotates sequence data, and provides them to the public via a website that contains a user-friendly search interface and a large number of sequence analysis tools, following the model of the highly regarded and widely used Los Alamos HIV database. The HCV website can be accessed via http://hcv.lanl.gov and http://hcv-db.org.

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Related in: MedlinePlus

Output of the Sequence Locator tool, which finds the location of a sequence fragment of any length. The graphic shows where the user's input sequence is located; the table beneath it shows the amino acid translation and coordinates of all of the genes included in the fragment.
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Figure 3: Output of the Sequence Locator tool, which finds the location of a sequence fragment of any length. The graphic shows where the user's input sequence is located; the table beneath it shows the amino acid translation and coordinates of all of the genes included in the fragment.

Mentions: Finally, a large number of tools are made available for manipulating or summarizing sequences. Some examples: ‘FindModel’ is a variation of Modeltest (16) a procedure that finds the evolutionary model that is most suitable for a given dataset and lists its parameters. ‘Gene Cutter’ is an HCV-specific tool that finds defined genes in a nucleotide input sequence, generates the appropriate amino acid translation, and is able to codon-align a set of sequences, which can then be downloaded. ‘Consensus’, a versatile tool to create consensus sequences of groups of sequences that can be modified by a large number of parameters. ‘Branchlength’ calculates the length of the branches in a tree between two nodes, or from a chosen node to the endnotes below it. It can also be used to re-root and plot a tree. ‘Sequence Locator’ is a program that finds the coordinates of an input sequence relative to the reference strain H77 (Figure 3). This program can be used as a means to standardize primer and epitope numbering, and quickly shows the user the location of an unknown HCV sequence fragment. It provides the amino acid translation in the correct frame if a nucleotide sequence was submitted, and aligns the amino acid sequence against the HCV-H77 nucleotide sequence if the input is an amino acid sequence. Sequence locator can also be used for reverse-complement sequences. ‘PeptGen’ is intended to help immunologists rationally design overlapping peptide sets to probe the immune response, taking into account forbidden N- and C-terminal amino acids and desired peptide length. ‘Primalign’ and ‘Epilign’ automatically align a primer or epitope to the HCV complete genome alignment. The interface returns the coordinates (H77 numbering) and an alignment of the fragment to all sequences in the whole genome alignment.Figure 3.


The hepatitis C sequence database in Los Alamos.

Kuiken C, Hraber P, Thurmond J, Yusim K - Nucleic Acids Res. (2007)

Output of the Sequence Locator tool, which finds the location of a sequence fragment of any length. The graphic shows where the user's input sequence is located; the table beneath it shows the amino acid translation and coordinates of all of the genes included in the fragment.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2238885&req=5

Figure 3: Output of the Sequence Locator tool, which finds the location of a sequence fragment of any length. The graphic shows where the user's input sequence is located; the table beneath it shows the amino acid translation and coordinates of all of the genes included in the fragment.
Mentions: Finally, a large number of tools are made available for manipulating or summarizing sequences. Some examples: ‘FindModel’ is a variation of Modeltest (16) a procedure that finds the evolutionary model that is most suitable for a given dataset and lists its parameters. ‘Gene Cutter’ is an HCV-specific tool that finds defined genes in a nucleotide input sequence, generates the appropriate amino acid translation, and is able to codon-align a set of sequences, which can then be downloaded. ‘Consensus’, a versatile tool to create consensus sequences of groups of sequences that can be modified by a large number of parameters. ‘Branchlength’ calculates the length of the branches in a tree between two nodes, or from a chosen node to the endnotes below it. It can also be used to re-root and plot a tree. ‘Sequence Locator’ is a program that finds the coordinates of an input sequence relative to the reference strain H77 (Figure 3). This program can be used as a means to standardize primer and epitope numbering, and quickly shows the user the location of an unknown HCV sequence fragment. It provides the amino acid translation in the correct frame if a nucleotide sequence was submitted, and aligns the amino acid sequence against the HCV-H77 nucleotide sequence if the input is an amino acid sequence. Sequence locator can also be used for reverse-complement sequences. ‘PeptGen’ is intended to help immunologists rationally design overlapping peptide sets to probe the immune response, taking into account forbidden N- and C-terminal amino acids and desired peptide length. ‘Primalign’ and ‘Epilign’ automatically align a primer or epitope to the HCV complete genome alignment. The interface returns the coordinates (H77 numbering) and an alignment of the fragment to all sequences in the whole genome alignment.Figure 3.

Bottom Line: The hepatitis C virus (HCV) is a significant public health threat worldwide.Presently, approximately 50 000 HCV sequences have been published.A central website that provides annotated sequences and analysis tools will be helpful to HCV scientists worldwide.

View Article: PubMed Central - PubMed

Affiliation: HCV database, Los Alamos National Laboratory, Los Alamos, NM, USA. kuiken@lanl.gov

ABSTRACT
The hepatitis C virus (HCV) is a significant public health threat worldwide. The virus is highly variable and evolves rapidly, making it an elusive target for the immune system and for vaccine and drug design. Presently, approximately 50 000 HCV sequences have been published. A central website that provides annotated sequences and analysis tools will be helpful to HCV scientists worldwide. The HCV sequence database collects and annotates sequence data, and provides them to the public via a website that contains a user-friendly search interface and a large number of sequence analysis tools, following the model of the highly regarded and widely used Los Alamos HIV database. The HCV website can be accessed via http://hcv.lanl.gov and http://hcv-db.org.

Show MeSH
Related in: MedlinePlus