Assists users in performing microbial genome annotation, data management and comparative analysis. MicroScope furnishes an environment permitting researchers to perform specifically comparative analysis of prokaryotic genomes, and manual curation of gene function in a comparative genomics and metabolic context. Moreover, this tool was used for annotating microbial genomes, transcriptomic and re-sequencing data.
A portable and easily configurable genome annotation pipeline. MAKER allows smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases. It identifies repeats, aligns ESTs and proteins to a genome, produces ab-initio gene predictions and automatically synthesizes these data into gene annotations having evidence-based quality values. MAKER's inputs are minimal and its ouputs can be directly loaded into a Generic Model Organism Database (GMOD). They can also be viewed in the Apollo genome browser; this feature of MAKER provides an easy means to annotate, view and edit individual contigs and BACs without the overhead of a database. MAKER is available for download and can be tested online via the MAKER Web Annotation Service (MWAS).
Helps in genome annotation. RATT is a software that allows users to transfer any entries from a reference sequence to similar samples. It can be applied to successive versions of a genome assembly, genomes of closely related species or strains. In addition, the software is also able to detect dissimilarities between two sequences and to generate inputs making genomes’ features to be visualized with Artemis. The software is a part of PAGIT toolkit.
Makes the annotation of novel plant genomes tractable for small groups with limited bioinformatics experience and resources, and faster and more transparent for large groups with more experience and resources. The MAKER-P pipeline generates species-specific repeat libraries, as well as structural annotations of protein coding genes, non-coding RNAs, and pseudogenes.
Follows the annotation graph approach, offering a unified graph-based representation. GenomeTools is a software library and an associated software tools for developing bioinformatics software intended to create, process or convert annotation graphs. To process large annotation sets with low memory overhead, the tool has been designed and implemented as an pull-based approach for sequential processing of annotations. This allows to handle even the largest annotation sets, such as a complete catalogue of human variations.
A web-based prokaryotic genome annotation server, which builds upon the Ergatis workflow system, integrates other dynamic analysis tools and provides intuitive web interfaces for biologists to customize and execute their own annotation pipelines. ISGA is designed to be installed at genomics core facilities and be used directly by biologists.
An integrated system for bacterial genome annotation. AGMIAL has been developed with the following requirements in mind: maximize annotation automation, ability to work on draft sequences, keep the program modular and extensible, choose informatics and bioinformatics standards when possible (e.g. Web Services, RDBMS, ...), distribute the program under an open-source license.