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Links tagged with 'viral genes'

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FluGenomeTool Content

http://www.flugenome.org/

Human Genome > Health and Disease
Model Organisms > Other Organisms
Sequence Comparison > Similarity Searching

FluGenome is a tool for determining lineages and genotypes of influenza A viruses.

NAR Web Server Issue 2007
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tagscomputational biology genetic databases genetic polymorphism genomics genotype influenza a virus orthomyxoviridae phylogeny viral genes viral genome viral proteins

GeminaDatabase Content

http://gemina.igs.umaryland.edu

Model Organisms > Databases

The Gemina system provides an integrated investigative and geospatial surveillance system connecting pathogens, pathogen products and disease anchored on the taxonomic ID of the pathogen and host to identify the breadth of hosts and diseases known for these pathogens, to identify the extent of outbreak locations, and to identify unique genomic regions with the DNA Signature Insignia Detection Tool.

NAR Database Issue 2010
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tagsanimals bacterial genes bacterial infections communicable diseases computational biology factual databases genetic databases humans nucleic acid databases viral genes virus diseases

GeneMarkTool Content

http://opal.biology.gatech.edu/GeneMark/

DNA > Gene Prediction

The GeneMark family of programs employ Markov models and are specifically tuned for gene prediction for sequences from prokaryotes, viral genomes and eukaryotes.

NAR Web Server Issue 2005
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tagsalgorithms animals bacterial genes computational biology genes genomics humans markov chains viral genes

Genotyping - NCBITool Content

http://www.ncbi.nih.gov/projects/genotyping/formpage.cgi

Model Organisms > Other Organisms
Sequence Comparison > Other Alignment Tools

The Genotyping tool at the NCBI identifies the genotype (or subtype) of viral sequences by using a sliding window approach to BLAST analysis against reference sequences for different viral subtypes. Results are shown as a graphical output plotting the top-scoring genotype. An alignment tool is also available.

NAR Web Server Issue 2004
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tagsalgorithms dna sequence analysis genetic recombination genotype hepacivirus hepatitis b virus hiv-1 molecular sequence data sequence alignment viral dna viral genes viral genome viruses
setsNational Center for Biotechnology Information (NCBI)

Influenza Virus ResourcesResource Content

http://www.ncbi.nlm.nih.gov/genomes/FLU/FLU.html

Model Organisms > Other Organisms

Influenza Virus Resource presents data obtained from the NIAID Influenza Genome Sequencing Project as well as from GenBank, combined with tools for flu sequence analysis and annotation. In addition, it provides links to other resources that contain flu sequences, publications and general information about flu viruses.

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tagsanimals genetic recombination genetic variation genome h3n2 subtype influenza a virus human influenza humans influenza a virus influenza vaccines influenza virus hemagglutinin glycoproteins molecular evolution mutagenesis mutation neuraminidase new york phylogeny public sector reassortant viruses sequence analysis time factors viral genes viral genome virus replication

NCBI Influenza Virus Sequence Annotation ToolTool Content

http://www.ncbi.nlm.nih.gov/genomes/FLU/Database/annotation.cgi

DNA > Annotations
DNA > Sequence Retrieval and Submission
Model Organisms > Other Organisms

The NCBI Influenza Virus Sequence Annotation Tool is a web application for user-provided sequences. It can predict protein sequences encoded by an input flu sequence and produce a feature table that can be used for sequence submission to GenBank.

NAR Web Server Issue 2007
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tagsalgorithms amino acid sequence dna sequence analysis genotype influenza a virus influenza b virus molecular sequence data sequence alignment viral dna viral genes viral genome viruses
setsNational Center for Biotechnology Information (NCBI)

PhEVERDatabase Content

http://pbil.univ-lyon1.fr/databases/phever

Model Organisms > Databases

The PhEVER database provides accurate evolutionary and phylogenetic information to analyse the nature of virus-virus and virus-host lateral gene transfers. It is a database of homologous families both (i) between sequences from different viruses and (ii) between viral sequences and sequences from cellular organisms. It offers a clustering of proteins into homologous families containing at least one viral sequences, as well as alignments and phylogenies for each of these families.

This content is being maintained by Leonor Palmeira.

NAR Database Issue 2011
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tagscluster analysis genetic databases genomics horizontal gene transfer host-pathogen interactions molecular evolution phylogeny sequence homology viral genes viral genome viral proteins viruses

Viral BioinformaticsTool Content

http://athena.bioc.uvic.ca/

Model Organisms > Other Organisms
Protein > Sequence Features
Sequence Comparison > Alignment Editing and Visualization
Sequence Comparison > Comparative Genomics
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Pairwise Sequence Alignments
Sequence Comparison > Similarity Searching

Viral Bioinformatics provides access to viral genomes and a variety of tools for comparative genomic analyses.

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tagsalgorithms amino acid sequence amino acid sequence homology animals bacterial genome base composition base sequence biological models canada capripoxvirus chlamydophila pneumoniae cluster analysis computational biology computer systems database management systems dna dna sequence analysis documentation factual databases fuzzy logic genetic databases genome genomics humans molecular evolution molecular sequence data multigene family multimedia mutation nucleic acid databases nucleic acid regulatory sequences nucleotides open reading frames phylogeny poxviridae programming languages protein databases protein sequence analysis reference standards sequence alignment statistical data interpretation systems integration technology transfer thermoplasma vaccinia virus variola virus viral dna viral genes viral genome viral proteins

ViralORFeomeDatabase Content

http://www.viralorfeome.com/

Model Organisms > Databases

ViralORFeome 1.0 is a database and management system that provides an integrated set of bioinformatic tools to clone viral ORFs in the Gateway(R) system. ViralORFeome provides a convenient interface to navigate through virus genome sequences, to design ORF-specific cloning primers, to validate the sequence of generated constructs and to browse established collections of virus ORFs. ViralORFeome has been designed to manage all possible variants or mutants of a given ORF so that the cloning procedure can be applied to any emerging virus strain. A subset of plasmid constructs generated with ViralORFeome platform has been tested with success for heterologous protein expression in different expression systems at proteome scale.

NAR Database Issue 2010
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tagscomputational biology genetic databases genetic techniques molecular cloning nucleic acid databases open reading frames protein databases tertiary protein structure viral genes viral genome