| Software name | Keywords | Description | Web ressources | Publications |
AlexSys : Alignment Expert System
 |
Multiple Alignment, Data mining, Machine learning, UIMA, Knowledge based system |
Although traditional bioinformatics analyses have provided the basis for the extraction of much useful information, today’s data-rich context means that the knowledge discovery process is complicated on the one hand, by the huge amount of heterogeneous data available, and on theother hand, by the next-to-impossible automation of the human expertise required. We developed a new knowledge-based expert system, AlexSys, for complex bioinformatics analyses and its subsequent application to a crucial task: Multiple Sequence Alignment. |
website |
PMID:18971242
PMID: 20530533 |
 |
ARP, Actin related proteins, prediction |
ARPAnno (Actin Related Proteins Annotation server) is a web tool that automatically annotates protein sequences according to the ARP classification. |
website |
PMID: 16195354 |
 |
BBS, MSA, alignment, Bardet Biedl Syndrome |
Bardet-Biedl Syndrome Bioinformatics resource. |
website |
PMID: 20177705
PMID: 16823392
PMID: 17160889
PMID: 16582908
|
 |
Oligonucleotide design, probe design, microarray, DNA chips |
CADO4MI (Computer Assisted Design of Oligonucleotide 4 MIcroarray) is a program for automatic design of oligonucleotides, fully customizable and accessible through a graphical user interface. For an input set of sequences, it allows parameter optimization and can combine multiple designs in distinct sequence databases. |
website |
PMID: 17727702 |
|
 Gscope
|
Genomics, integrative software plateform |
Gscope is an integrated platform allowing the analysis of all kind of genomic data. It is written in Tcl/Tk and runs on all plateforms. It is specially designed to perform high throughput analysis. Gscope is mainly composed of tools necessary to create the basic data, analysis tools, visualisation interfaces. It allows also the creation and feeding of SQL relational databases and the quering and display of the available information through a web based interface (Wscope). |
Gscope server |
|
 |
Protein family analysis, multiple sequence alignment, sequence annotation |
MACSIMS (Multiple Alignment of Complete Sequences Information Management System) is a multiple alignment-based information management system that combines the advantages of both knowledge-based and ab initio sequence analysis methods. Structural and functional information is mined automatically from the public databases. In the MACS, homologous regions are identified and the mined data is evaluated and propagated from known to unknown sequences with these reliable regions. MACSIMS provides a unique environment that facilitates knowledge extraction and the presentation of the most pertinent information to the biologist. |
website |
PMID: 16792820 |
 |
Orthology, Inparalogy, Vizualisation |
OrthoInspector is a software system incorporating an original algorithm for the rapid detection of orthology and inparalogy relations between different species. IIn addition, several visualization tools have been developed to facilitate in-depth studies based on these predictions. It is made available as an independent software suite that can be downloaded and installed for local use. Command line querying facilitates the integration of the software in high throughput processing pipelines and a graphical interface provides easy, intuitive access to results for the non-expert. |
website |
PMID: 21219603
|
 |
Protein family analysis, multiple sequence alignment, database search |
PipeAlign is an on-line protein family analysis tool providing both interactive and automatic workbench for the validation, integration and presentation of the biological insights resulting from the analysis. It integrates a 5 step process ranging from the search for sequence homologues in protein sequence and 3D structure databases to the definition of the hierarchical relationship between and within subfamilies. Each step relies upon the results from the previous ones until a validated multiple alignment integrating subfamilies information is produced. The Pipe can also be started from any point and intermediate results are easily consulted. |
website |
PMID: 12824430 |
|
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automatic report, statitical analysis, R, Bioconductor, microarray, TCA |
The aim of RReportGenerator consists in providing a simple and user-friendly graphical user interface (GUI) allowing to run routine statistical analysis using R via predefined analysis scenarios in a local and independent manner. Of course, the large variety of additional libraries on CRAN and Bioconductor may be used with the analysis scenarios. The results (text, figures and tables) are automatically assembled into a report in pdf- (or dvi) format. This may be accompanied by an additional file(s) for exporting (specific) results to other applications (spread-sheet programs, web-browser etc). |
website
sourceforge |
PMID: 18037684 |
