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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.
We have described in the paper Reticulate representation of evolutionary and functional relationships between phage genomes, Lima-Mendez et al., Mol Biol Evol, 2008 (see the Publications page) a method to represent the evolutionary relationships among all the viruses in ACLAME. We have integrated the method in the ACLAME analysis pipeline to generate the reticulate classification of the MGE in all ACLAME categories (Plasmids, Viruses, Viruses and prophages and All). At present, each MGE view features an additional tab, called MGE Classification, giving access to its reticulate classifications. Additional tools will be made available on the ACLAME web site in the coming weeks for more extented use of the reticulate classifications.
Based on the idea that genes with similar profile occurrence across genomes are likely involved in the same function (Pellegrini et al, PNAS 1999 96(8):4285-4288), we have generated evolutionary cohesive modules (ECM) using the hypergeometric formula for phylogenetic profiles comparisons and MCL for clustering the profiles within all ACLAME categories. The MGE view features an additional tab, called MGE ECM, that allows to display the modules where the MGE proteins belong to. Analysis on the MGE ECM indicates that they are associated to particular a functional class, host group or MGE type/group.
With the release of ACLAME 0.4, improvements have been made on the web site to facilitate the navigation and special attention was made on browsers compatibility. Users of FireFox 3.x, InternetExplorer 7.x and 8.x, Safari 4.x, Opera 6.x, GoogleChrome 3.x and Konqueror 4.x should get all or most of the site content properly displayed.
11 December 2008: Web pages fixes for Internet Explorer
Some users reported difficulties to navigate the ACLAME web site with Internet Explorer. We strongly recommend to use a descent web browser such as FireFox (see the Mozilla web site) in order to display properly the ACLAME web site content. However, we have modified several sections of the web site in order to make the web pages properly displayed in Internet Explorer.
9 December 2008: Reference MGEs
We have started to define some MGEs as reference entries. Such MGEs have their proteins description re-annotated with the latest and most up-to-date known information. MGEs tagged as reference have the Reference MGE icon icon shown on the ACLAME web site.
10 November 2008: Improved Blast requests management
A new system has been implemented to handle the Blast search requests. The previous system was occasionally blocked when too many requests were made at the same time. This problem should not happen anymore.
10 September 2008: Downloading ACLAME data in MS Excel format
It is now possible to download data from ACLAME using the Microsoft Excel format. The option is available in the Download section of the web site and in several other places where data can be downloaded.
9 September 2008: Improvements on the web site navigation
Some improvements have been made on the ACLAME web interface to facilitate the navigation and to visualise more easily some pages content. Among the improvements, simple links have been replaced with buttons and some data are now presented in folding boxes (with a +/- icon to expand/collapse the boxes). Comments on the ACLAME web site are welcome for further improvements.
31 July 2008: Prophinder exports in GFF
A new option has been added to the Prophinder web site to download predictions in GFF format.
22 May 2008: ACLAME source code cleaning
A big cleaning has been made in the source code used for the ACLAME web site and tools. With the continuous addition of analysis and navigation tools, the underlying code became a bit patchy. The cleaning consisted in regrouping portions on the code and rationalising some decision trees. The work affect all the ACLAME web site sections. A throughout test of the site has been made but some problems might show up. Please report any problem you might encounter while browsing the web site or using the online tools.
1 May 2008: Added an exporter tool to the Blast results page
It is now possible to export the ACLAME Blast search results. The exporter tool offer at present two options: 1) download of the raw Blast output 2) a tab-delimited table with a number of customizable fields. The table file can be loaded in any spreadsheet program.
30 April 2008: Advanced MGE filtering tool
MGEs can be filtered based on their host taxonomy. The page listing the MGEs has a new filter tool that can accept keywords to be matched with taxonomical entry names or NCBI taxon IDs. After typing the keywords, you can wait for search results from the NCBI taxonomy database and select from the results list a specific entry to be used as filter. Otherwise, after typing the keywords, you can immediately apply the filter (click on the 'filter' button). Applying the filter will display only MGEs with a host name matching the entered keywords or selected from the taxo search results list.
22 April 2008: Additional family exporter tool
A new tool called 'Genes in FASTA' has been added in the family viewer. It allows to download the genes coding for the proteins present in the displayed family.
21 April 2008: Updated keywords search engine
A new version of the keywords search engine has been installed. The search includes now the MeGO and GO ontologies, MGE genes and additional new fields in other DB components. The search speed has been significantly increased as well.
17 April 2008: Extended Blast interface
We have extended functionalities in the Blast interface to accept amino acid and DNA sequences as input. It is also possible to search against the ACLAME proteins or genes. The Blast result page provide more information as well, including which MGE the hit sequences belong to.
26 February 2008: ACLAME version 0.3 is out!
ACLAME version 0.3 is finally out! The database contains 1109 plasmids and 457 viruses.
Protein families have been generated using a slightly improved procedure where the all-vs-all comparison is now performed using the ssearch program for better quality alignments and therefore more homogeneous families.
A large number of plasmid and virus families have been annotated. The annotations are now based on the GeneOntology and our local mobile genetic elements ontology, called MeGO.
The ACLAME relational database schema has been extended in order to accommodate elements composed of several DNA segments. Genes are now integrated in the database and proteins (CDS) have their genomic range included too.
Many improvements have been made as well on the web interface to facilitate the navigation in the ACLAME database.
Additional tools have been added to easily export data from the ACLAME database.
Database searches against NCBI-NR, SwissProt and SCOP have been made for all single proteins. HMM searches with the ACLAME families are still going on and the results will be added to the server upon completion.
An newer version of the forums management (phpBB) has been installed. If you wish to contribute to the improvement of any aspect of ACLAME or report problems, please register and post your comments!
26 February 2008: New hardware
A new machine has been installed for the ACLAME server. It is a dual core pentium processor running at 3.2GHz with 4GB of memory. The new system should be capable to handle the ever increasing requests to the ACLAME server and related projects such as Prophinder and MeGO.
15 January 2008: Prophinder is out!
Prophinder is a tool dedicated to the detection of prophages in sequenced bacterial genomes.
You can either browse the Prophinder database which contains pre-calculated predictions for a large number of sequenced bacterial genomes. The database will be updated regularly for newly sequenced genomes. You can also submit your own genome in GenBank format and get back the predictions. A web service is provided to integrate Prophinder in automatic annotation pipelines.
20 March 2007: PhiGO: the Phage Gene Ontology
We have started to work on a Gene Ontology dedicated to phage functions called PhiGO. The idea is to collect all known phage functions in this ontology following the same schema as the official Gene Ontology (see the Gene Ontology web site for more information). Whenever we reach a milestone in the development of PhiGO, the GO terms will be transferred to the official Gene Ontology. You can access the OBO files and the AmiGO web interface at the PhiGO page.
19 March 2007: Full implementation of GO in ACLAME
We have fully integrated the Gene Ontology (GO) in ACLAME. The ontology is downloaded from the GO web site (http://www.geneontology.org) and loaded in a MySQL database on the ACLAME web server. Protein families annotated with an ACLAME function cross-linked to GO or simply annotated with a GO function will be displayed with an icon (Tooltip) that will popup the GO term definition.
6 February 2007: An ACLAME exporter tool
We have added a new tool used to export data from the ACLAME database in tab-delimited text format. The exported files can be loaded directly in spreadsheet programs for futher manipulation. The exporter can be accessed from the navigation menu on the page left side.
5 February 2007: Improved search engine
The search engine on the ACLAME web site has been improved by adding a recognition of entries ID which will forward you directly to the matching page. For nstance, entering a keyword like 'protein:vir:3422' or like 'mge:70' will bring you directly to the matching protein or MGE page respectively.
24 November 2006: Multiple sequence alignment with Jalview
It is now possible to view the multiple sequence alignment of a family using Jalview (http://www.jalview.org). You need Java to be installed on your computer and activated in your browser. Once these requirements are met, you will see a MSA with Jalview button in all pages showing protein families.
9 November 2006: Major upgrade of the ACLAME database.
The ACLAME database has been ported to the PostgreSQL database management system (DBMS). This major upgrade was necessary in order to cope with the increased amount and complexity of the data store in the ACLAME database. The new DBMS should also provide faster access to the ACLAME content.
The web site has been updated to access the data through the new DBMS as well, however the web site layout has been kept (almost) identical, it is only the tools in the background that have been changed.
We have also implemented a more advanced user management system. From now on, you can register on the ACLAME web site for participating to the annotation of ACLAME protein families or single proteins. Anonymous annotations are accepted as well. We hope that some of you will take the time to add such annotations to enrich and improve the data quality in ACLAME.
More information will be posted in the news in the coming days to present other new features implemented in ACLAME. There might be some glitches left in the tools, please report any problem you might encounter while browsing the web site.
We hope that you'll continue to enjoy visiting our web site and start contributing actively to the project.
Best regards,
       The ACLAME Team.
29 August 2006: Works planned on the server
Works will be done on the ACLAME server in the coming days. Expect some interruptions of the services or slower responses. A new message will be posted once the works will be over. Sorry for any inconveniences.
29 March 2005: Cluster export in FASTA format
A new tool has been added in the cluster content view interface to export the sequences in FASTA format. Click on the FASTA button to download the sequences in FASTA format.
24 March 2005: Function definitions bug fixed
A bug in the database management system used for ACLAME was found to be responsible to corrupt ACLAME function definitions. A workaround has been implemented to resolve the problem.
Some function corruptions might still be left in the database, these will be fixed as soon as possible.
22 December 2004: Powercut stranded the ACLAME server
A powercut put the ACLAME web server offline Wed Dec 22 2004 from 12:00 to 15:30 CET (UTC/GMT +1 hour). The server is now up and running again.
20 December 2004: Added FASTA format in the protein sequence viewer
In the single protein view, it is now possible to display the sequence in FASTA format. A button has been added to switch between the 'Fasta format' and the 'Simple format'.
13 December 2004: Pre-calculated DB statistics
The detailed statistics about the database content are now pre-calculated for faster access. The information will be updated on a daily basis which means a maximum of 24 hours delay for changes in the database to be included in the statistics.
8 December 2004: New search engine
A new search engine has been developed in order to facilitate the access of ACLAME information. The search engine is accessible from the home page, in the genome viewer and in the protein viewer. It can take one or several keywords and search the ACLAME database for matching entries. The search engine can also recognise ACLAME identifiers such as 'vir:protein:108', 'genome:6', 'host:55', 'cluster:all:98' or even 'cluster:98'.
The results are shown in a table with the first column describing the type of entry and the second column the match and a link to the entry.
6 July 2004: New MSA viewer
A new multiple sequence alignment viewer has been implemented. The new features are:
- change of the alignment wrapping size
- colored mode is now an image instead of an html table
- change of the font size.
25 June 2004: More statistics
More statistics about the database content are available from the More stats link in the home page. The information provided include an overview of the database evolution throughout the versions, the general composition of the DB version being accessed, some basic frequencies concerning the clusters and the functional annotations. Note that the statistics are generated on-the-fly which requires a bit of time before being displayed, be a bit patient.
24 June 2004: More information from functions list
In the list of ACLAME functions used for the annotation, an extra column with a [+] sign has been added. By following the link, all the clusters or all the proteins being annotated with the given function will be enumerated.
18 May 2004: ACLAME version 0.2 is out!
ACLAME version 0.2 contains the viruses found in 0.1 plus more than 500 plasmids. Functional annotation for viruses and plasmid clusters is available separately. The clusters for both MGEs categories combined (category 'All') is also available but without functional annotation yet.
Several improvements for browsing ACLAME has been made with this new release. Associated with most table column headers, a triangle pointing downward has been added, use it to sort the tables either in an increasing or decreasing order.
A new help system has been implemented to facilitate the navigation. When an entry has a link with a question mark next to it, point your mouse over it to get a popup window with a description related to that entry. Click on the link to get a permanent window.
Extra work has been done to make the navigation, data retrieval and web page rendering even more faster. Some glitches might still be around, please let us know if something goes wrong.
10 February 2004: ACLAME in NAR 2004 DB issue
The ACLAME article in the annual issue on databases of Nucleic Acid Research has been published and is available online for reading.
See the paper on the NAR Web site
3 February 2004: ACLAME version 0.1 is out!
ACLAME version 0.1 is an update of version alpha with more viral genomes. When browsing the classification you can choose the version you want to access from the top navigation menu in the web pages.
The web server is also running on a new faster computer.
4 November 2003: Secondary structures prediction
We have run the Psi-pred secondary structures prediction on the ACLAME protein sequences. In the protein view, you can now switch to the 'Secondary structure prediction' view. Example: vir:protein:2585
4 November 2003: Improved clusters browsing
We separated the 'big' clusters (3 or more proteins) from the 'small' clusters (less than 3 proteins). You can switch between them using the top right option in the page. For each cluster view it is also possible to move to the next/previous one or jump to a given cluster ID.
29 September 2003: ACLAME server hardware is moving
Our lab is reoganising servers for improved network protection. ACLAME server will physically be moved to a new location, expect to find it momentarily down between Mon 29 and Tue 30 Septembre 2003.
4 August 2003: Update DB engine and sequences IDs
We have implemented a faster procedure to access or retrieve information from the ACLAME database. Protein IDs have been updated to include the genome type. In this case, all proteins of the first dataset are from viruses, therefore they all have 'vir:' as prefix in their IDs.
10 July 2003: Browsing tools open
A first set of tools used to browse the ACLAME database are now accessible. Expect some glitches to occur.
23 January 2003: Aclame web site online
The Aclame web site is now open to public access. The site is still under development, expect more pages and services in the near future.