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Links tagged with 'viral genome'

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DNASU Plasmid RepositoryDatabase Content

http://dnasu.asu.edu/DNASU/ [open in a new window]

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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).

links directory index: 3
TitlePublication YearGoogle Scholar Citation Count
Protein Structure Initiative Material Repository: an open shared public resource of structural genomics plasmids for the biological community20103
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/ [open in a new window]

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

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

links directory index: 41
TitlePublication YearGoogle Scholar Citation Count
FluGenome: a web tool for genotyping influenza A virus200741
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

Gene3DDatabase Content

http://gene3d.biochem.ucl.ac.uk/ [open in a new window]

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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.

links directory index: 22
TitlePublication YearGoogle Scholar Citation Count
Gene3D: a domain-based resource for comparative genomics, functional annotation and protein network analysis.20122
Gene3D: merging structure and function for a Thousand genomes201020
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 [open in a new window]

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Model Organisms > Other Organisms

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

links directory index: 363
TitlePublication YearGoogle Scholar Citation Count
Methods for optimizing antiviral combination therapies200342
Geno2pheno: Estimating phenotypic drug resistance from HIV-1 genotypes2003147
Diversity and complexity of HIV-1 drug resistance: a bioinformatics approach to predicting phenotype from genotype2002174
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

GWIDDDatabase Content

http://gwidd.bioinformatics.ku.edu [open in a new window]

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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.

links directory index: 11
TitlePublication YearGoogle Scholar Citation Count
GWIDD: Genome-wide protein docking database201011
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 [open in a new window]

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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.

links directory index: 714
TitlePublication YearGoogle Scholar Citation Count
The web server of IBM's Bioinformatics and Pattern Discovery group: 2004 update20044
The web server of IBM's Bioinformatics and Pattern Discovery group20039
Dictionary-driven prokaryotic gene finding200241
Dictionary-driven protein annotation200237
The emergence of pattern discovery techniques in computational biology200092
Building dictionaries of 1D and 3D motifs by mining the Unaligned 1D sequences of 17 archaeal and bacterial genomes.19990
Combinatorial pattern discovery in biological sequences: The TEIRESIAS algorithm1998531
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 [open in a new window]

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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.

links directory index: 498
TitlePublication YearGoogle Scholar Citation Count
Whole-genome analysis of human influenza A virus reveals multiple persistent lineages and reassortment among recent H3N2 viruses2005222
Large-scale sequencing of human influenza reveals the dynamic nature of viral genome evolution2005276
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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

Integrated Microbial Genomes (IMG)Database Content

http://img.jgi.doe.gov/ [open in a new window]

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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.

links directory index: 110
TitlePublication YearGoogle Scholar Citation Count
IMG: the Integrated Microbial Genomes database and comparative analysis system20123
The integrated microbial genomes system: an expanding comparative analysis resource2010107
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 [open in a new window]

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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.

links directory index: 14
TitlePublication YearGoogle Scholar Citation Count
IRESite--a tool for the examination of viral and cellular internal ribosome entry sites201014
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

MAVIDTool Content

http://bio.math.berkeley.edu/mavid/download/ [open in a new window]

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DNA > Phylogeny Reconstruction
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Multiple Sequence Alignments

MAVID performs multiple sequence alignments for large sequences, constructs phylogenetic trees and displays VISTA plots of conserved regions.

links directory index: 329
TitlePublication YearGoogle Scholar Citation Count
MAVID: constrained ancestral alignment of multiple sequences2004260
MAVID multiple alignment server200369
NAR Web Server Issue 2003
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tagsanimals base sequence cats cattle computational biology conserved sequence cystic fibrosis transmembrane conductance regulator dna sequence analysis dogs fishes genome genomics hiv-1 human genome humans mice molecular evolution molecular sequence data phylogeny rabbits rats sequence alignment simian immunodeficiency virus swine takifugu viral genome

MEROPSDatabase Content

http://merops.sanger.ac.uk/ [open in a new window]

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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.

links directory index: 283
TitlePublication YearGoogle Scholar Citation Count
MEROPS: the database of proteolytic enzymes, their substrates and inhibitors201211
MEROPS: the peptidase database2010272
NAR Database Issue 2010
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external linksLink on Wikipedia
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

MetaBioMEDatabase Content

http://metasystems.riken.jp/metabiome/ [open in a new window]

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Protein > Databases

MetaBioiME is a web resource to find novel homologs for known Commercially Useful Enzymes (CUEs) in metagenomic datasets and completed bacterial genomes.

This content is being maintained by tdtaylor.

links directory index: 11
TitlePublication YearGoogle Scholar Citation Count
MetaBioME: a database to explore commercially useful enzymes in metagenomic datasets201011
NAR Database Issue 2010
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tagsanimals bacterial genome computational biology genetic databases humans natural language processing nucleic acid databases open reading frames protein databases sequence alignment tertiary protein structure viral genome

MetaCycDatabase Content

http://metacyc.org/ [open in a new window]

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Protein > Databases

The MetaCyc database is a comprehensive resource for metabolic pathways and enzymes from all domains of life. The pathways in MetaCyc are experimentally determined, small-molecule metabolic pathways and are curated from the primary scientific literature. Pathways reactions are linked to one or more well-characterized enzymes, and both pathways and enzymes are annotated with reviews, evidence codes, and literature citations.

links directory index: 493
TitlePublication YearGoogle Scholar Citation Count
The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases.201236
The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases2010457
NAR Database Issue 2010
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tagsanimals archaeal genome bacterial genome biological models computational biology genetic databases humans nucleic acid databases plant genome protein databases tertiary protein structure viral genome

MINTDatabase Content

http://mint.bio.uniroma2.it/mint/ [open in a new window]

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Protein > Databases
Protein > Networks & Interactions, Pathways and Enzymes

MINT is a public repository for molecular interactions reported in peer-reviewed journals. MINT has adopted the PSI-MI standards for the annotation and for the representation of molecular interactions and is a member of the IMEx consortium.

links directory index: 685
TitlePublication YearGoogle Scholar Citation Count
MINT, the molecular interaction database: 2009 update2010149
MINT: a Molecular INTeraction database2002536
NAR Database Issue 2010
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tagsanimals computational biology epidermal growth factor receptor genetic databases humans nucleic acid databases programming languages protein binding protein databases protein interaction mapping tertiary protein structure viral genome

NBRP resourcesDatabase Content

http://www.nig.ac.jp/database/index-e.html [open in a new window]

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Literature > Databases

The National BioResource Project (NBRP) is a system for collecting, preserving and providing bioresources for use as experimental materials for life science research. Thirty databases and an integrated database-retrieval system (BioResource World: BRW) have been created. BRW provides access to a collection of 4.5-million records on bioresources including wild species, inbred lines, mutants, genetically engineered lines, DNA clones, etc. BRW supports summary browsing, keyword searching, and searching by DNA sequences or gene ontology. The results of searches provide links to online requests for distribution of research materials.

links directory index: 11
TitlePublication YearGoogle Scholar Citation Count
NBRP databases: databases of biological resources in Japan201011
NAR Database Issue 2010
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tagsalgorithms animals computational biology gene expression profiling genetic databases humans japan nucleic acid databases plant genome protein databases viral genome

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