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Links tagged with 'archaeal genome'

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CodonOTool Content

http://digbio.missouri.edu/software/index.html [open in a new window]

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DNA > Structure and Sequence Feature Detection
Model Organisms > General Resources

CodonO is a method for measuring synonymous codon usage bias within and across genomes.

links directory index: 63
TitlePublication YearGoogle Scholar Citation Count
CodonO: codon usage bias analysis within and across genomes200722
Quantitative relationship between synonymous codon usage bias and GC composition across unicellular genomes200441
NAR Web Server Issue 2007
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tagsarchaeal dna archaeal genome bacterial dna bacterial genome base composition codon computational biology computer simulation gc rich sequence genetic code genetic models genome species specificity

COMBREXDatabase Content

http://combrex.bu.edu [open in a new window]

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Model Organisms > Databases

COMBREX is a project to increase the speed of the functional annotation of new bacterial and archaeal genomes. It consists of a database of functional predictions produced by computational biologists and a mechanism for experimental biochemists to bid for the validation of those predictions. Small grants are available to support successful bids.

links directory index: 11
TitlePublication YearGoogle Scholar Citation Count
COMBREX: a project to accelerate the functional annotation of prokaryotic genomes201111
NAR Database Issue 2011
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tagsarchaeal genome bacterial genome genetic databases genomics molecular sequence annotation protein databases

GC-ProfileTool Content

http://tubic.tju.edu.cn/GC-Profile/ [open in a new window]

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DNA > Structure and Sequence Feature Detection

GC-Profile is a web-based tool for visualizing and analyzing the variation of GC content in genomic sequences.

links directory index: 45
TitlePublication YearGoogle Scholar Citation Count
GC-Profile: a web-based tool for visualizing and analyzing the variation of GC content in genomic sequences200631
Segmentation algorithm for DNA sequences200514
NAR Web Server Issue 2006
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tagsalgorithms animals archaeal genome automated pattern recognition bacterial genome base composition base sequence chickens chromosome mapping cpg islands cytosine dna dna sequence analysis genetic models genomic islands genomics guanine isochores molecular sequence data sequence alignment statistical models

GDAPTool Content

http://www.doe-mbi.ucla.edu/Services/GDAP [open in a new window]

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Protein > Biochemical Features
Protein > Sequence Features

The Genomic Disulfide Analysis Program (GDAP) predicts disulfide bonds for a user-supplied protein sequence. GDAP also provides access to pre-computed predictions of disulfide bonds for over 100 microbial genomes.

links directory index: 24
TitlePublication YearGoogle Scholar Citation Count
GDAP: a web tool for genome-wide protein disulfide bond prediction200424
NAR Web Server Issue 2004
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tagsarchaeal genome archaeal proteins bacterial genome bacterial proteins cysteine disulfides protein sequence analysis statistical data interpretation

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

GOLDDatabase Content

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

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DNA > Databases
Model Organisms > Databases
Model Organisms > General Resources

The Genomes On Line Database (GOLD) is a comprehensive resource for centralized monitoring of genome and metagenome projects worldwide. Both complete and ongoing projects, along with their associated metadata, can be accessed in GOLD through precomputed tables and a search page. GOLD is in accordance with the Minimum Information about a (Meta)Genome Sequence (MIGS/MIMS) specification.

links directory index: 239
TitlePublication YearGoogle Scholar Citation Count
The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata20128
The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata2010231
NAR Database Issue 2010
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tags20th century history 21st century history animals archaeal genome bacterial genome computational biology environmental microbiology factual databases genetic databases genome genomics human genome project humans information storage and retrieval international cooperation internet metagenomics nucleic acid databases online systems phylogeny protein databases software systems integration tertiary protein structure user-computer interface

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

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

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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external linksLink on Wikipedia
tagsanimals archaeal genome bacterial genome biological models computational biology genetic databases humans nucleic acid databases plant genome protein databases tertiary protein structure viral genome

MicroFootPrinterTool Content

http://bio.cs.washington.edu/MicroFootPrinter.html [open in a new window]

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DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Model Organisms > Microbes
Sequence Comparison > Comparative Genomics

MicroFootPrinter identifies the conserved motifs in regulatory regions of prokaryotic genomes using the phylogenetic footprinting program FootPrinter.

links directory index: 598
TitlePublication YearGoogle Scholar Citation Count
MicroFootPrinter: a tool for phylogenetic footprinting in prokaryotic genomes200623
FootPrinter: A program designed for phylogenetic footprinting2003161
Algorithms for phylogenetic footprinting2002146
Discovery of regulatory elements by a computational method for phylogenetic footprinting2002268
NAR Web Server Issue 2006
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tagsalgorithms amino acid sequence homology animals archaeal genome bacterial genome computational biology conserved sequence dna footprinting dna sequence analysis fish proteins fos genes genetic promoter regions genomics growth hormone humans insulin interleukin-3 introns metallothionein multigene family myc genes nucleic acid databases nucleic acid regulatory sequences nucleic acid sequence homology phylogeny regulator genes transcriptional regulatory elements

MiSTDatabase Content

http://genomics.ornl.gov/mist/ [open in a new window]

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Model Organisms > Databases
Protein > Databases

The MiST2 database identifies and catalogs the repertoire of signal transduction proteins in microbial genomes. These are identified by searching protein sequences for specific domain profiles that implicate a protein in signal transduction. MiST2 contains a host of new features and improvements including the following: draft genomes; extracytoplasmic function (ECF) sigma factor protein identification; enhanced classification of signaling proteins; novel, high-quality domain models for identifying histidine kinases and response regulators; neighboring two-component genes; gene cart; better search capabilities; enhanced taxonomy browser; advanced genome browser; and a modern, biologist-friendly web interface.

links directory index: 35
TitlePublication YearGoogle Scholar Citation Count
The MiST2 database: a comprehensive genomics resource on microbial signal transduction201035
NAR Database Issue 2010
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tagsarchaea archaeal genome archaeal proteins bacteria bacterial genome bacterial proteins computational biology genetic databases protein databases signal transduction tertiary protein structure

P2CSDatabase Content

http://www.p2cs.org [open in a new window]

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Protein > Databases

P2CS is a database for prokaryotic two-component systems (TCSs). The database annotates and classifies TCS proteins from completely sequenced prokaryotic genomes and metagenomes. TCS complements can be browsed by metagenome, replicon or sequence cluster (and these genesets are available for download by users). A variety of database-wide or taxon-specific searches are also supported. Each TCS protein is fully annotated with sequence-feature information including replicon context, while properties of the predicted proteins can be queried against several external prediction servers to suggest homologues, interaction networks, sub-cellular localization and domain complements. There is also a CGView representation of the distribution of TCS genes around a replicon, categorization of TCS genes based on gene organization, an expanded domain-based classification scheme, a P2CS 'gene cart' and categorization on the basis of sequence clusters.

links directory index: 5
TitlePublication YearGoogle Scholar Citation Count
P2CS: a database of prokaryotic two-component systems20115
NAR Database Issue 2011
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external linksLink on Wikipedia
tagsarchaeal genome archaeal proteins bacterial genome bacterial proteins intercellular signaling peptides and proteins molecular sequence annotation protein databases protein kinases

PfamDatabase Content

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

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Protein > Databases

Pfam is a database of protein families and domains. The database uses HMMER3, the latest version of the popular profile hidden Markov model package. Pfam release 24.0 contains 11,912 families.

links directory index: 11859
TitlePublication YearGoogle Scholar Citation Count
The Pfam protein families database.2012212
The Pfam protein families database.20101375
The Pfam protein families database.20081524
Pfam: clans, web tools and services.20061648
The Pfam protein families database.20042639
The Pfam protein families database.20022079
The Pfam protein families database.20001281
Pfam 3.1: 1313 multiple alignments and profile HMMs match the majority of proteins.1999545
Pfam: multiple sequence alignments and HMM-profiles of protein domains.1998556
NAR Database Issue 2010
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tagsalgorithms amino acid sequence amino acid sequence homology animals archaeal genome binding sites caenorhabditis elegans computational biology computer communication networks computer graphics encyclopedias as topic factual databases fungal genome genome genomics humans information storage and retrieval internet macromolecular substances markov chains molecular evolution molecular models molecular sequence data multigene family nucleic acid databases phylogeny protein conformation protein databases protein sequence analysis proteins quality control secondary protein structure sequence alignment software statistics as topic tertiary protein structure user-computer interface

REBASEDatabase Content

http://rebase.neb.com/rebase/rebase.html [open in a new window]

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Protein > Databases

REBASE is a comprehensive database of information about restriction enzymes, DNA methyltransferases and related proteins involved in the biological process of restriction-modification (R-M). It contains fully referenced information about recognition and cleavage sites, isoschizomers, neoschizomers, commercial availability, methylation sensitivity, crystal and sequence data. Experimentally characterized homing endonucleases are also included.

links directory index: 101
TitlePublication YearGoogle Scholar Citation Count
REBASE--a database for DNA restriction and modification: enzymes, genes and genomes2010101
NAR Database Issue 2010
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tagsarchaeal genome bacterial genome binding sites computational biology dna modification methylases dna restriction enzymes genetic databases genomics protein databases substrate specificity tertiary protein structure

TADBDatabase Content

http://bioinfo-mml.sjtu.edu.cn/TADB/ [open in a new window]

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Other Molecules > Databases

TADB is an integrated database that provides comprehensive information about Type 2 toxin-antitoxin (TA) loci. TADB offers both predicted and experimentally supported Type 2 TA loci-relevant data. A broad range of similarity search, sequence alignment, genome context browser and phylogenetic tools are readily accessible via TADB.

links directory index: 14
TitlePublication YearGoogle Scholar Citation Count
TADB: a web-based resource for Type 2 toxin-antitoxin loci in bacteria and archaea201114
NAR Database Issue 2011
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tagsarchaea archaeal genome archaeal proteins bacteria bacterial genome bacterial proteins bacterial toxins biological toxins genetic databases genetic loci

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