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ACLAME: Home Page

A CLAssification of Mobile genetic Elements. BiGRe - Service de Bioinformatique des Génomes et des Réseaux. ACLAME is a database dedicated to the collection and classification of mobile genetic elements (MGEs) from various sources, comprising all known phage genomes, plasmids and transposons. In addition to provide information on the full genomes and genetic entities, it aims at building a comprehensive classification of the functional modules of MGE's at the protein, gene, and higher levels. We have sta...

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ACLAME: Home Page | aclame.ulb.ac.be Reviews
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A CLAssification of Mobile genetic Elements. BiGRe - Service de Bioinformatique des Génomes et des Réseaux. ACLAME is a database dedicated to the collection and classification of mobile genetic elements (MGEs) from various sources, comprising all known phage genomes, plasmids and transposons. In addition to provide information on the full genomes and genetic entities, it aims at building a comprehensive classification of the functional modules of MGE's at the protein, gene, and higher levels. We have sta...
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2 classification
3 phage
4 plasmid
5 transposon
6 pathogenicity island
7 genomic island
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ACLAME: Home Page | aclame.ulb.ac.be Reviews

https://aclame.ulb.ac.be

A CLAssification of Mobile genetic Elements. BiGRe - Service de Bioinformatique des Génomes et des Réseaux. ACLAME is a database dedicated to the collection and classification of mobile genetic elements (MGEs) from various sources, comprising all known phage genomes, plasmids and transposons. In addition to provide information on the full genomes and genetic entities, it aims at building a comprehensive classification of the functional modules of MGE's at the protein, gene, and higher levels. We have sta...

INTERNAL PAGES

aclame.ulb.ac.be aclame.ulb.ac.be
1

ACLAME: Hosts list

http://aclame.ulb.ac.be/perl/Aclame/Genomes/hosts_view.cgi

Burkholderia cepacia genomovar I. Pseudomonas cepacia (ex Burkholder 1950) Palleroni and Holmes 1981. Burkholderia cepacia (Palleroni and Holmes 1981) Yabuuchi et al. 1993. Pseudomonas cepacia" Burkholder 1950. Pseudomonas multivorans" Stanier et al. 1966. Lactobacillus casei subsp. casei. Salmonella typhi-murium" (sic) (Loeffler 1892) Castellani and Chalmers 1919. Bacillus typhimurium" Loeffler 1892. Salmonella choleraesuis serotype typhimurium. Spiroplasma Saglio et al. 1973. Bacillus coli" Migula 1895.

2

ACLAME: MeGO

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

MeGO is a Gene Ontology under construction dedicated to the functions of mobile genetic elements. The terms defined in MeGO are used to annotate phage and plasmid protein families in ACLAME. Please note that some terms in the ontology are there transiently as markers or awaiting future incorporation in the sequence ontology. The phage ontology PhiGO has now been incorporated in MeGO and can thus be accessed in MeGO version 1.0 and up. From this page you can:. Or the MySQL dump.

3

ACLAME: News

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

5 August 2009: ACLAME version 0.4 is out! The three major new features are: 1) addition of prophages in the database, 2) access to the reticulate classification and 3) access to the evolutionary cohesive modules. Prophages have been selected from the best Prophinder predictions (see Prophinder web site. The selection was based on the significance score and with some manual curation. A category Viruses and prophages. Has been added to access the combined set of viruses and prophages. Based on the idea tha...

4

ACLAME: Prophinder

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

Prophinder is a tool dedicated to the detection of prophages in sequenced bacterial genomes. The algorithm uses the coding sequences (CDS) that are similar (using BLASTP) to phage proteins stored in the ACLAME. Distributing Prophinder as a standalone application is not possible due to many dependencies. The web service should provide identical functionality with the advantage of always using the most up-to-date version of the program and annotations in the ACLAME database. Predictions in bacterial genomes.

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LINKS TO THIS WEBSITE

phage-list.blogspot.com phage-list.blogspot.com

Phage-list: Welcome to phage-list

http://phage-list.blogspot.com/2009/01/welcome-to-phage-list.html

Saturday, January 24, 2009. Phage-list is the unimaginative name I've set up for a group blog for phage biologists. It was inspired by thinking that some of the discussion on the phage list. Listserv would make good blog posts. So I'm setting this up and inviting members of the list to blog - and/or provide links to other sites. Subscribe to: Post Comments (Atom). A Classification of Mobile Elements (ACLAME). ASM Division M HomePhage. HHMI Science Education Alliance Phage project.

phage-list.blogspot.com phage-list.blogspot.com

Phage-list: Horizontal gene transfer in the Scientific American 60-second podcast

http://phage-list.blogspot.com/2009/01/horizontal-gene-transfer-in-scientific.html

Saturday, January 24, 2009. Horizontal gene transfer in the Scientific American 60-second podcast. View or listen here. Subscribe to: Post Comments (Atom). A Classification of Mobile Elements (ACLAME). ASM Division M HomePhage. HHMI Science Education Alliance Phage project. The Bacteriophage Ecology Group. Horizontal gene transfer in the Scientific America.

phage-list.blogspot.com phage-list.blogspot.com

Phage-list: M13 and bioengineering

http://phage-list.blogspot.com/2009/01/m13-and-bioengineering.html

Saturday, January 24, 2009. Reports on using phage display to make scaffolds for tissue engineering. Subscribe to: Post Comments (Atom). A Classification of Mobile Elements (ACLAME). ASM Division M HomePhage. HHMI Science Education Alliance Phage project. The Bacteriophage Ecology Group. Horizontal gene transfer in the Scientific America.

gydb.org gydb.org

Gypsy Database 2.0

http://www.gydb.org/index.php/GINGER1

GIN/GINGER TRs and INTs. Clan AA Ref. DB. Cores Seq. DB. Genome Seq. DB. LTRs and TIRs Seq. DB. Mobile Group II introns DB. Tree of Life Project. From The Gypsy Database. Gypsy-Integrase-Related Type 1 ( GINGER1. Is a recently described pool of exon-intron transposons ( Bao et al. Which encode for a transposase (TR) showing the occurrence of a GPY/F module ( Malik and Eickbush 1999. Thought to mediate multimerization ( Ebina et al. At its C-terminus. GINGER1. Cysteine protease domain, or an Ulp1. Element...

gydb.org gydb.org

Gypsy Database 2.0

http://www.gydb.org/index.php/Retroviridae

GIN/GINGER TRs and INTs. Clan AA Ref. DB. Cores Seq. DB. Genome Seq. DB. LTRs and TIRs Seq. DB. Mobile Group II introns DB. Tree of Life Project. From The Gypsy Database. Evolutionary history and viral taxonomy:. Vertebrate retroviruses ( Retroviridae. Originally received attention when infectious representatives were characterized in humans. However, it is now known that any LTR retrotransposon capable of recruiting a third ORF envelope gene ( env. Is potentially capable of becoming a retrovirus ( env.

gydb.org gydb.org

Gypsy Database 2.0

http://www.gydb.org/index.php/GINA

GIN/GINGER TRs and INTs. Clan AA Ref. DB. Cores Seq. DB. Genome Seq. DB. LTRs and TIRs Seq. DB. Mobile Group II introns DB. Tree of Life Project. From The Gypsy Database. Is a recently described pool of exon-intron transposons ( Marin 2010. Which encode for a transposase (TR) showing the occurrence of a GPY/F module ( Malik and Eickbush 1999. Thought to mediate multimerization ( Ebina et al. At its C-terminus. GINA. Cysteine protease domain, or an Ulp1. Protease catalytic domain ( Marin 2010. Elements ar...

gydb.org gydb.org

Gypsy Database 2.0

http://www.gydb.org/index.php/GINNY

GIN/GINGER TRs and INTs. Clan AA Ref. DB. Cores Seq. DB. Genome Seq. DB. LTRs and TIRs Seq. DB. Mobile Group II introns DB. Tree of Life Project. From The Gypsy Database. Is a recently described pool of exon-intron transposons ( Marin 2010. Which encode for a transposase (TR) showing the occurrence of a GPY/F module ( Malik and Eickbush 1999. Thought to mediate multimerization ( Ebina et al. At its C-terminus. GINNY. Cysteine protease domain, or an Ulp1. Protease catalytic domain ( Marin 2010. Elements a...

gydb.org gydb.org

Gypsy Database 2.0

http://www.gydb.org/index.php/Bel/Pao

GIN/GINGER TRs and INTs. Clan AA Ref. DB. Cores Seq. DB. Genome Seq. DB. LTRs and TIRs Seq. DB. Mobile Group II introns DB. Tree of Life Project. From The Gypsy Database. Evolutionary history and in-progress taxonomy:. LTR retroelements ( Malik et al. Constitute a family of LTR retrotransposons and retroviruses described to date only in metazoan genomes ( Copeland et al. This family was originally characterized with the discovery of element sequences such as Pao. Davis and Judd 1995. And the various Cer.

gydb.org gydb.org

Gypsy Database 2.0

http://www.gydb.org/index.php/Retroelements

GIN/GINGER TRs and INTs. Clan AA Ref. DB. Cores Seq. DB. Genome Seq. DB. LTRs and TIRs Seq. DB. Mobile Group II introns DB. Tree of Life Project. From The Gypsy Database. Tyrosine recombinase (YR) retroelements. Retroelements (retrotransposons and retroviruses) can currently be divided into four systems or groups commonly known as the long terminal repeat (LTR) retroelements. Eickbush and Jamburuthugoda 2008. Genes, and env. Families (for more details, see LTR retroelements. On the basis of their molecul...

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ACLAME

Post your comments to the ACLAME Blog. Post your comments to the ACLAME Blog.

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ACLAME

Post your comments to the ACLAME Blog. Post your comments to the ACLAME Blog.

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ACLAME: Home Page

A CLAssification of Mobile genetic Elements. BiGRe - Service de Bioinformatique des Génomes et des Réseaux. ACLAME is a database dedicated to the collection and classification of mobile genetic elements (MGEs) from various sources, comprising all known phage genomes, plasmids and transposons. In addition to provide information on the full genomes and genetic entities, it aims at building a comprehensive classification of the functional modules of MGE's at the protein, gene, and higher levels. We have sta...

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