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Links tagged with 'viruses'

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CVTreeTool Content

http://tlife.fudan.edu.cn/cvtree

Model Organisms > Microbes
Protein > Phylogeny Reconstruction

Composition Vector Tree (CVTree) infers phylogenetic relationships between microbial organisms by comparing their proteomes using a composition vector approach.

NAR Web Server Issue 2004NAR Web Server Issue 2009
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tagsalgorithms archaeal genome bacteria bacterial genome chloroplast dna fungal genome genome genomics phylogeny viral genome viruses

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)

InsigniaTool Content

http://insignia.cbcb.umd.edu

Model Organisms > Microbes
Sequence Comparison > Comparative Genomics

Insignia provides a web interface for identifying unique genomic signatures from a database of all current bacterial and viral genomic sequences. Input is any set of target and background genomes.

NAR Web Server Issue 2009
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tagsanimals bacteria bacterial genome dna sequence analysis humans infection viral genome viruses

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

ViralZoneDatabase Content

http://www.expasy.org/viralzone/

Model Organisms > Databases

ViralZone web resource provides fact sheets on all known virus families/genera with easy access to sequence data. A selection of reference strains (RefStrain) provides annotated standards to circumvent the exponential increase of virus sequences. ViralZone offers a complete set of detailed and accurate virion pictures.

NAR Database Issue 2011
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tagsgenetic databases genomics proteomics viral genome viral proteins virion virus physiological phenomena virus replication viruses

Virus Genotyping ToolsTool Content

http://bioafrica.mrc.ac.za/rega-genotype/html/

DNA > Phylogeny Reconstruction
Model Organisms > Microbes

This web server facilitates high-throughput virus genotyping by aligning query sequences to a pre-defined set of reference strains and then computing phylogenetic analysis.

NAR Web Server Issue 2009
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tagsbase sequence genetic recombination genetic variation genotype hepacivirus hepatitis b virus hiv-1 phylogeny reference standards sequence alignment sequence analysis viruses