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Links tagged with 'bacteriophages'

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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

PHIRETool Content

http://www.biw.kuleuven.be/logt/PHIRE.htm

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation

Phage In silico Regulatory Elements (PHIRE) is a standalone program in Visual Basic which performs a string-based search on bacteriophage genome sequences discovering and extracting blocks displaying sequence similarity corresponding to conserved regulatory elements contained within these genomes.

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tagsbacteriophages base sequence dna sequence analysis gene expression profiling molecular sequence data nucleic acid sequence homology regulator genes sequence alignment viral gene expression regulation viral genome

phiSITEDatabase Content

http://www.phisite.org

Model Organisms > Databases

phiSITE is a database of gene regulation in bacteriophages. It collects experimentally confirmed or predicted regulatory elements (promoters, operators, terminators and attachment sites) from bacteriophages belonging to Siphoviridae, Myoviridae and Podoviridae families. The database is manually curated, the data are collected mainly form scientific papers, cross-referenced with other database resources (EMBL, UniProt, NCBI taxonomy database, NCBI Genome, ICTVdb, PubMed Central).

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NAR Database Issue 2010
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tagsbacteriophages computational biology nucleic acid databases viral gene expression regulation viral genome