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Links tagged with 'plasmids'

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ACLAMEDatabase Content

http://aclame.ulb.ac.be/

DNA > Databases

The ACLAME database is dedicated to the collection, analysis and classification of sequenced mobile genetic elements (MGEs, in particular phages and plasmids). Classifications are available at various levels of organization. At the gene/protein level, families group similar sequences that are expected to share the same function. Families of four or more proteins are manually assigned with a functional annotation using the GeneOntology and the locally developed ontology MeGO dedicated to MGEs. At the genome level, evolutionary cohesive modules group sets of protein families shared among MGEs. At the population level, networks display the reticulate evolutionary relationships among MGEs.

NAR Database Issue 2010
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tagsalgorithms bacterial genome bacteriophages computational biology genetic databases interspersed repetitive sequences nucleic acid databases nucleic acid repetitive sequences plasmids

BASysTool Content

http://basys.ca

DNA > Annotations
Model Organisms > Microbes

BASys (Bacterial Annotation System) is a tool for automated annotation of bacterial genomic (chromosomal and plasmid) sequences including gene/protein names, GO functions, COG functions, possible paralogues and orthologues, molecular weights, isoelectric points, operon structures, subcellular localization, signal peptides, transmembrane regions, secondary structures, 3-D structures, reactions, and pathways.

This content is being maintained by gary.vandomselaar@gmail.com.

NAR Web Server Issue 2005
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tagsbacterial chromosomes bacterial genome genomics plasmids

CGView ServerTool Content

http://stothard.afns.ualberta.ca/cgview_server/

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

The CGView Server generates graphical maps of circular genomes that can be used to visualize sequence conservation in the context of sequence features, imported analysis results, open reading frames and base composition plots. The server uses BLAST to compare the primary sequence of up to three genomes or sequence sets, aiding in the identification of conserved genome segments, instances of horizontal transfer or visualization of genome segments from newly obtained sequence reads.

This content is being maintained by jason.grant.

NAR Web Server Issue 2008
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tagsbacterial genome chloroplast genome chromosome mapping circular dna genomics mitochondrial genome plasmids sequence alignment

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

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

NEBcutterTool Content

http://tools.neb.com/NEBcutter/index.php3

DNA > Tools For the Bench

NEBcutter finds non-overlapping open reading frames and sites for all enzymes that cut the sequence just once; max length is 100 kb.

NAR Web Server Issue 2003
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tagsdna methylation dna restriction enzymes dna sequence analysis plasmids restriction mapping substrate specificity type ii site-specific deoxyribonucleases

PlasMapperTool Content

http://wishart.biology.ualberta.ca/PlasMapper/index.html

DNA > DNA and Genomic Analysis
DNA > Tools For the Bench

Web server that automatically generates and annotates circular plasmid maps. The tool has: a built in set of features that can be displayed (ie. RE sites, tags, ORFs, etc.); allows users to define custom features to display; contains a library of commonly used plasmids; and, generates nice looking images in a variety of output formats.

NAR Web Server Issue 2004
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tagschromosome mapping dna sequence analysis plasmids restriction mapping

taveRNATool Content

http://compbio.cs.sfu.ca/taverna/

RNA > Functional RNAs
RNA > Structure Prediction, Visualization, and Design

taveRNA hosts three RNA web services: alteRNA, inteRNA and pRuNA. alteRNA is an alternative to many RNA folding methods. inteRNA predicts the joint secondary structure of two RNA sequences. pRuNA is an database pruning method which given a query RNA returns only a few ncRNAs as potential regulators.

NAR Web Server Issue 2007
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tagsadenosine triphosphatases algorithms antisense rna bacterial genome bacterial rna base sequence binding sites cation transport proteins chemical models computational biology computer simulation escherichia coli escherichia coli proteins humans molecular sequence data nucleic acid conformation plasmids programming languages rna rna sequence analysis rna stability sequence alignment statistical models trans-activators

TRODTool Content

http://www.cellbio.unige.ch/RNAi.html

DNA > Tools For the Bench
Expression > Gene Regulation
RNA > Structure Prediction, Visualization, and Design

T7 RNAi Oligo Designer (TROD) aids in the design of DNA oligonucleotides for short interfering RNA (siRNA) synthesis with T7 RNA polymerase. It takes an input of a cDNA sequence and outputs a list of DNA oligos for ordering.

NAR Web Server Issue 2004
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tagscell line dna-directed rna polymerases double-stranded rna gene silencing green fluorescent proteins hela cells humans luminescent proteins messenger rna molecular cloning molecular sequence data oligodeoxyribonucleotides plasmids recombinant fusion proteins rna interference small interfering rna transfection viral proteins

WEB-THERMODYNTool Content

http://www.gsa.buffalo.edu/dna/dk/WEBTHERMODYN/

DNA > Structure and Sequence Feature Detection

WEB-THERMODYN analyzes DNA sequences and computes the DNA helical stability. This tool can be used to predict sites of low helical stability present at regulatory regions for transcription and replication.

NAR Web Server Issue 2003
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tagsdeoxyribonucleases dna dna replication dna sequence analysis fungal chromosomes fungal dna mutation nucleic acid conformation nucleic acid denaturation nucleic acid regulatory sequences plasmids replication origin replicon saccharomyces cerevisiae thermodynamics