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Comparative Genomics

General resources for comparison of sequences and genomes.

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Displaying 15 links

GenomeTraFaCTool Content

http://genometrafac.cchmc.org/genome-trafac/index.jsp [open in a new window]

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DNA > Structure and Sequence Feature Detection
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Comparative Genomics

GenomeTraFaC is a comparative genomics based resource for initial characterization of gene models and the identification of putative cis-regulatory regions of RefSeq gene orthologs.

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links directory index: 20
TitlePublication YearGoogle Scholar Citation Count
GenomeTrafac: a whole genome resource for the detection of transcription factor binding site clusters associated with conventional and microRNA encoding genes conserved between mouse and human gene orthologs200720
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InsigniaTool Content

http://insignia.cbcb.umd.edu [open in a new window]

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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.

links directory index: 12
TitlePublication YearGoogle Scholar Citation Count
Insignia: a DNA signature search web server for diagnostic assay development200912
NAR Web Server Issue 2009
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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

ISC Large-scale Sequencing Project DatabaseDatabase Content

http://www.intlgenome.org/viewDatabase.cfm [open in a new window]

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Model Organisms > General Resources
Sequence Comparison > Comparative Genomics

The International Sequencing Consortium (ISC) Large-scale Sequencing Project Database contains information on current and completed sequencing projects, including project timelines, funding agencies, sequencing strategy and links out to project web pages.

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JGI Genome PortalDatabase Content

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

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DNA > Annotations
DNA > DNA and Genomic Analysis
DNA > Databases
Sequence Comparison > Comparative Genomics

The JGI Genome Portal provides a unified access point to all JGI genomic databases and analytical tools. A user can find all DOE JGI sequencing projects and their status, search for and download assemblies and annotations of sequenced genomes, and interactively explore those genomes and compare them with other sequenced microbes, fungi, plants or metagenomes using specialized systems tailored to each particular class of organisms.

links directory index: 3
TitlePublication YearGoogle Scholar Citation Count
The genome portal of the Department of Energy Joint Genome Institute20123
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KAASTool Content

http://www.genome.jp/kegg/kaas/ [open in a new window]

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DNA > Annotations
Protein > Networks & Interactions, Pathways and Enzymes
Sequence Comparison > Comparative Genomics

KAAS (KEGG Automatic Annotation Server) is a tool for ortholog assignment and pathway mapping. KAAS provides functional annotation of genes by BLAST comparisons against the manually curated KEGG GENES database. The result contains KO (KEGG Orthology) assignments and automatically generated KEGG pathways.

links directory index: 168
TitlePublication YearGoogle Scholar Citation Count
KAAS: an automatic genome annotation and pathway reconstruction server2007168
NAR Web Server Issue 2007
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tagsanimals artificial intelligence automation chromosome mapping computational biology controlled vocabulary database management systems documentation genome humans proteome sequence analysis signal transduction

KOMODOResource Content

http://www.pggenetica.icb.ufmg.br/komodo/ [open in a new window]

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Sequence Comparison > Comparative Genomics

Kegg Orthology enrichMent - Online DetectiOn (KOMODO) webserver detects significantly under- or over-represented groups of homologous genes (KO groups) in one taxon when compared with another taxon in a given biochemical pathway. It also displays the results in the form of a dynamically generated webpage that contains visual information about the pathway surveyed.

links directory index: not available
TitlePublication YearGoogle Scholar Citation Count
NAR Web Server Issue 2012
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MauveTool Content

http://gel.ahabs.wisc.edu/mauve/ [open in a new window]

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Sequence Comparison > Alignment Editing and Visualization
Sequence Comparison > Comparative Genomics
Sequence Comparison > Multiple Sequence Alignments

Mauve is a stand-alone software tool for constructing multiple genome alignments.

links directory index: 590
TitlePublication YearGoogle Scholar Citation Count
progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement2010112
Mauve: multiple alignment of conserved genomic sequence with rearrangements2004478
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tagsalgorithms bacterial chromosomes bacterial dna bacterial genome computer simulation conserved sequence enterobacteriaceae escherichia coli escherichia coli o157 gene rearrangement genetic recombination salmonella typhi salmonella typhimurium sequence alignment shigella flexneri software design software validation species specificity theoretical models

METAGENassistTool Content

http://www.metagenassist.ca [open in a new window]

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Model Organisms > Microbes
Sequence Comparison > Comparative Genomics

METAGENassist is a statistical tool for comparative metagenomics. Users upload bacterial census data from 16S rRNA or sequencing experiments.

links directory index: not available
TitlePublication YearGoogle Scholar Citation Count
NAR Web Server Issue 2012
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mGenomeSubtractorTool Content

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

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Model Organisms > Microbes
Sequence Comparison > Comparative Genomics

mGenomeSubtractor performs mpiBLAST-based comparison of reference bacterial genomes against multiple user-selected genomes. Such in silico subtractive hybridization also allows for definition of species-specific gene pools and can be used to develop genomic arrays.

links directory index: 12
TitlePublication YearGoogle Scholar Citation Count
mGenomeSubtractor: a web-based tool for parallel in silico subtractive hybridization analysis of multiple bacterial genomes201012
NAR Web Server Issue 2010
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tagsbacterial genes bacterial genome genomics oligonucleotide array sequence analysis sequence alignment species specificity

MGIPTool Content

http://mgip.biology.gatech.edu [open in a new window]

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DNA > Mapping and Assembly
Human Genome > Health and Disease
Model Organisms > Microbes
Sequence Comparison > Comparative Genomics
Sequence Comparison > Pairwise Sequence Alignments

The Meningococcus Genome Informatics Platform (MGIP) is a suite of computational tools for the analysis of multilocus sequence typing data. Input DNA sequence files are analyzed to provide allele calls, and to characterize the specific sequence type and clonal complex of the Neisseria meningitidis strain.

links directory index: 4
TitlePublication YearGoogle Scholar Citation Count
Meningococcus genome informatics platform: a system for analyzing multilocus sequence typing data20094
NAR Web Server Issue 2009
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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

MIPSDatabase Content

http://www.helmholtz-muenchen.de/en/ibis [open in a new window]

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Model Organisms > General Resources
Model Organisms > Other Organisms
Model Organisms > Plants
Model Organisms > Yeast
Protein > Networks & Interactions, Pathways and Enzymes
Sequence Comparison > Comparative Genomics

Munich Information Centre for Protein Sequences projects include: fungal genome analysis, plant genome bioinformatics, structural genomics, proteomics and genome annotation. Projects and databases include: CYGD, MNCDB, NGFN, MPPI, SIMAP, QUIPOS, MATDB, MOsDB, SPUTNIK, and PEDANT.

links directory index: 703
TitlePublication YearGoogle Scholar Citation Count
MIPS: curated databases and comprehensive secondary data resources in 201020119
MIPS: analysis and annotation of proteins from whole genomes2004422
MIPS Arabidopsis thaliana Database (MAtDB): an integrated biological knowledge resource for plant genomics200487
MOsDB: an integrated information resource for rice genomics200317
Sputnik: a database platform for comparative plant genomics200350
The PEDANT genome database2003118
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external linksLink on Wikipedia
tagsanimals arabidopsis arabidopsis proteins biological models complementary dna computational biology data mining dna transposable elements expressed sequence tags fungi gene duplication genetic databases genome genomics humans information storage and retrieval internet metabolomics mice micrornas neoplasm genes nucleic acid databases nucleic acid sequence homology oryza sativa phenotype plant genes plant genome protein binding protein databases protein interaction mapping protein sequence analysis proteins proteomics saccharomyces cerevisiae proteins sequence homology software systems integration user-computer interface

mirEXDatabase Content

http://comgen.pl/mirex/ [open in a new window]

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Expression > Gene Regulation
RNA > Databases
Sequence Comparison > Comparative Genomics

mirEX is a comprehensive platform for comparative analysis of primary microRNA expression data.

links directory index: 1
TitlePublication YearGoogle Scholar Citation Count
mirEX: a platform for comparative exploration of plant pri-miRNA expression data20121
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MLSTTool Content

http://www.mlst.net/ [open in a new window]

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DNA > Phylogeny Reconstruction
Model Organisms > Microbes
Sequence Comparison > Comparative Genomics

MLST (Multi Locus Sequence Typing) is a nucleotide sequence based approach for the unambiguous characterisation of isolates of bacteria and other organisms using the sequences of internal fragments of seven house-keeping genes.

links directory index: 2035
TitlePublication YearGoogle Scholar Citation Count
The multilocus sequence typing network: mlst.net200589
Molecular typing of bacteria directly from cerebrospinal fluid200043
Multilocus sequence typing: molecular typing of bacterial pathogens in an era of rapid DNA sequencing and the internet1999136
Multilocus sequence typing: a portable approach to the identification of clones within populations of pathogenic microorganisms19981767
NAR Web Server Issue 2005
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tagsalleles bacteria bacterial dna bacterial genes bacterial meningitis bacterial typing techniques cerebrospinal fluid cluster analysis dna sequence analysis evaluation studies as topic gene frequency humans meningococcal infections molecular sequence data mycological typing techniques neisseria meningitidis nucleic acid databases pneumococcal meningitis polymerase chain reaction serotyping streptococcus pneumoniae virulence

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