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Links tagged with 'viral genome'

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Found 29 links

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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

DNASU Plasmid RepositoryDatabase Content

http://dnasu.asu.edu/DNASU/

DNA > Databases

DNASU is a central repository for plasmid clones and collections. DNASU currently stores and distributes over 130,000 plasmids including over 45,000 human and mouse plasmids, full genome collections from numerous organisms, and the protein expression plasmids from the Protein Structure Initiative (PSI).

NAR Database Issue 2010
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tagsanimals bacterial genome computational biology genetic databases humans nucleic acid databases plasmids protein databases tertiary protein structure viral genome

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

GenBankDatabase Content

http://www.ncbi.nlm.nih.gov

DNA > Databases

GenBank is a comprehensive database that contains publicly available nucleotide sequences for more than 300,000 organisms named at the genus level or lower, obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects, including whole genome shotgun (WGS) and environmental sampling projects. Daily data exchange with the European Molecular Biology Laboratory Nucleotide Sequence Database in Europe and the DNA Data Bank of Japan ensures worldwide coverage. GenBank is accessible through the NCBI Entrez retrieval system, which integrates data from the major DNA and protein sequence databases along with taxonomy, genome, mapping, protein structure and domain information, and the biomedical journal literature via PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases.

NAR Database Issue 2010NAR Database Issue 2011
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tagsalgorithms animals bacterial genome computational biology expressed sequence tags genetic databases genomics high-throughput nucleotide sequencing humans metagenomics molecular sequence annotation national institutes of health (u.s.) national library of medicine (u.s.) nucleic acid databases plant genome protein databases united states viral genome

Gene3DDatabase Content

http://gene3d.biochem.ucl.ac.uk/

Protein > Databases

Gene3D provides accurate structural domain family assignments for over 1100 genomes and nearly 10,000,000 proteins. A hidden Markov model library, constructed from the manually curated CATH structural domain hierarchy, is used to search UniProt, RefSeq and Ensembl protein sequences. The resulting matches are refined into simple multi-domain architectures. The domain assignments are integrated with multiple external protein function descriptions (e.g. Gene Ontology and KEGG), structural annotations (e.g. coiled coils, disordered regions and sequence polymorphisms) and family resources (e.g. Pfam and eggNog). Gene3D also provides a set of services, including an interactive genome coverage graph visualizer, DAS annotation resources, sequence search facilities and SOAP services.

NAR Database Issue 2010
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tagsalgorithms animals archaeal genome bacterial genome computational biology dna sequence analysis genetic databases humans markov chains nucleic acid databases protein databases tertiary protein structure viral genome

Geno2phenoTool Content

http://www.geno2pheno.org/cgi-bin/geno2pheno.pl

Model Organisms > Other Organisms

Geno2pheno takes as input an HIV-1 pol-gene DNA sequence and estimates phenotypic drug resistance to 17 antiretroviral drugs.

NAR Web Server Issue 2003
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tagsalgorithms anti-hiv agents artificial intelligence automated pattern recognition cluster analysis computational biology computer-assisted drug therapy computing methodologies decision trees disease susceptibility dna sequence analysis drug combinations factual databases gene expression profiling genetic models genetic polymorphism genetic variation genotype hiv hiv infections hiv-1 humans innate immunity molecular sequence data phenotype pol genes regression analysis reproducibility of results sensitivity and specificity statistical models viral dna viral drug resistance viral genome

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)

GWIDDDatabase Content

http://gwidd.bioinformatics.ku.edu

Protein > Databases

Genome-wide docking database (GWIDD) is an integrated resource for structural studies of protein-protein interactions on the genome scale, which combines the available experimental data with models obtained by docking techniques. Current database version (August 2009) contains 25 559 experimental and modeled 3D structures for 771 organisms spanned over the entire universe of life from viruses to humans. Data are organized in a relational database with user-friendly search interface allowing exploration of the database content by a number of parameters. Search results can be interactively previewed and downloaded as PDB-formatted files, along with the information relevant to the specified interactions.

NAR Database Issue 2010
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tagsanimals computational biology genetic databases genome humans nucleic acid databases protein databases protein interaction mapping tertiary protein structure viral genome viral proteins

IBM Bioinformatics and Pattern Discovery GroupTool Content

http://cbcsrv.watson.ibm.com/Tspd.html

DNA > Annotations
DNA > Gene Prediction
DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Human Genome > Annotations
Protein > 2-D Structure Prediction
Protein > Annotation and Function
Protein > Biochemical Features
Protein > Domains and Motifs
RNA > Motifs
Sequence Comparison > Multiple Sequence Alignments

Extensive server possessing a wide range of tools for pattern discovery in DNA and protein sequences as well as in text. Tools for multiple sequence alignment, gene discovery, protein annotation, and other applications also exist on this server. A detailed help page is provided for all tools.

NAR Web Server Issue 2003NAR Web Server Issue 2004
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tagsalgorithms amino acid motifs amino acid sequence amino acid sequence homology animals anti-infective agents archaeal genes archaeal genome automated pattern recognition bacterial genes bacterial genome base sequence biomedical engineering chemical dictionaries computational biology conserved sequence dna dna sequence analysis eukaryotic cells evaluation studies as topic factual databases gene expression genetic databases genome genomics histones humans initiator codon leghemoglobin molecular models molecular sequence data open reading frames peptides probability protein databases protein sequence analysis proteins proteome rna sequence analysis secondary protein structure sequence alignment sequence analysis ubiquitin viral genome

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

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

Integrated Microbial Genomes (IMG)Database Content

http://img.jgi.doe.gov/

DNA > Annotations
Model Organisms > Databases
Model Organisms > Microbes
Sequence Comparison > Comparative Genomics

The integrated microbial genomes (IMG) system serves as a community resource for comparative analysis of publicly available genomes in a comprehensive integrated context. IMG contains both draft and complete microbial genomes integrated with other publicly available genomes from all three domains of life, together with a large number of plasmids and viruses. IMG provides tools and viewers for analyzing and reviewing the annotations of genes and genomes in a comparative context.

NAR Database Issue 2010
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tagsarchaeal genome bacterial genome computational biology genetic databases nucleic acid databases plasmids protein databases tertiary protein structure viral genome

IRESiteDatabase Content

http://www.iresite.org

RNA > Databases

The IRESite presents carefully curated experimental evidence of many eukaryotic viral and cellular internal ribosome entry site (IRES) regions. The IRESite tool provides biologically meaningful information regarding the IRESs and their experimental background (including annotation of IRES secondary structures and IRES trans-acting factors). RNA secondary structures and for searching through the structures currently stored in the database can also be done.

NAR Database Issue 2010
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tagsanimals computational biology dna sequence analysis genetic databases humans nucleic acid conformation nucleic acid databases plasmids ribosomes translational peptide chain initiation viral genome viral rna

jpHMMTool Content

http://jphmm.gobics.de/

Model Organisms > Microbes
Model Organisms > Other Organisms

Jumping Profile Hidden Markov Model (jpHMM) takes a HIV-1 genome sequence and uses a pre-calculated multiple alignment of the major HIV-1 subtypes to predict the phylogenetic breakpoints and HIV subtype of the submitted sequence.

This content is being maintained by akschultz.

NAR Web Server Issue 2006NAR Web Server Issue 2009
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tagsalgorithms amino acid sequence homology base sequence dna breaks genetic recombination genomics hiv-1 markov chains phylogeny proteins reproducibility of results sequence alignment tertiary protein structure viral genome

MEROPSDatabase Content

http://merops.sanger.ac.uk/

Protein > Databases

The MEROPS database is a collection of peptidases. The database has a hierarchical classification in which homologous sets of peptidases and protein inhibitors are grouped into protein species, which are grouped into families, which are in turn grouped into clans. The database can distinguish one peptidase from another through identifying the specificity of the peptidase in terms of where it will cleave substrates and with which inhibitors it will interact.

NAR Database Issue 2010
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tagsamino acid sequence amino acid sequence homology animals archaeal proteins computational biology genetic databases genomics humans molecular sequence data peptide hydrolases protein databases tertiary protein structure viral genome