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Links tagged with 'archaeal genome'

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Found 19 links

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CodonOTool Content

http://digbio.missouri.edu/software/index.html

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

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

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

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.

NAR Database Issue 2011
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tagsarchaeal genome bacterial genome genetic databases genomics molecular sequence annotation protein databases

CRISPRFinderTool Content

http://crispr.u-psud.fr/Server/CRISPRfinder.php

DNA > Structure and Sequence Feature Detection
Model Organisms > Microbes

Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) Finder detects this family of direct repeats found in the DNA of many bacteria and archaea.

NAR Web Server Issue 2007
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tagsalgorithms archaeal genome bacterial genome chromosome mapping computational biology database management systems genetic databases intergenic dna nucleic acid repetitive sequences

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

GC-ProfileTool Content

http://tubic.tju.edu.cn/GC-Profile/

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.

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

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.

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/

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

GOLDDatabase Content

http://www.genomesonline.org/

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.

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

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

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

IslandPathTool Content

http://www.pathogenomics.sfu.ca/islandpath/

DNA > Annotations
DNA > Structure and Sequence Feature Detection
Model Organisms > Microbes

IslandPath aids genomic island detection in prokaryotic genome seqeunces, using features such as dinucleotide bias, G+C, location of tRNA genes, annotations of mobility genes, etc. Genomic islands are defined here as genomic regions of potential horizontal origin.

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tagsarchaea archaeal genome bacteria bacterial genome cpg islands database management systems dna sequence analysis horizontal gene transfer phylogeny sequence alignment

MetaCycDatabase Content

http://metacyc.org/

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.

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

Microbe BrowserTool Content

http://microbe.vital-it.ch

Model Organisms > Microbes

The Microbe Browser is a web server providing comparative microbial genomics data integrated from GenBank, RefSeq, UniProt, InterPro, Gene Ontology and the Orthologs Matrix Project (OMA) databases. Gene predictions based on 5 software packages is also displayed.

NAR Web Server Issue 2009
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tagsarchaeal genome bacterial chromosomes bacterial genome genomics

MicroFootPrinterTool Content

http://bio.cs.washington.edu/MicroFootPrinter.html

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.

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/

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.

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