:: DESCRIPTION
Genome Randomizer is a simple utility to generate random sequences from complete prokaryotic genomes using 11 different stochastic models.
::DEVELOPER
Computational Microbiology Laboratory
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
The GRC (Genome Reverse Compiler) is an annotation tool for prokaryotic genomes. Its name and philosophy are based on analogy with a high-level, programming language compiler.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
The Genome Reverse Compiler: an explorative annotation tool.
Warren AS, Setubal JC.
BMC Bioinformatics. 2009 Jan 27;10:35. doi: 10.1186/1471-2105-10-35.
:: DESCRIPTION
Gecko is a further development of the original Gecko software. It allows for the systematic detection of gene cluster conservation in a large number of genomes. The enhancement over the original Gecko tool is the use of set-distance based gene cluster models that allow for the detection of gene clusters with diverse conservation patterns including gaps and missing genes in cluster occurrences. It is also tolerant of errors in gene homology assignment.
::DEVELOPER
Katharina Jahn and Leon Kuchenbecker
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Computation of median gene clusters
S. Böcker, K. Jahn, J. Mixtacki, and J. Stoye. J. Comp. Biol., 16(8):1085-1099, 2009.
:: DESCRIPTION
MED is a non-supervised prokaryotic gene prediction method which integrates MED2.0 and TriTISA, an iterative self-learning translation initiation site (TIS) prediction algorithm. As the update of MED2.0, MED 2.1 modifies the TIS model by replacing the previous one to TriTISA, which imoroves the prediction accuracies for both 3′ and 5′ ends.
::DEVELOPER
ZhuLab, Peking Uiniversity, Beijing
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Zhu,H.Q. et al. 2007
MED: a new non-supervised gene prediction algorithm forbacterial and archaeal genomes.
BMC Bioinformatics,8, 97
Gangqing,Hu. Et al. 2009.
Prediction of translation initiation site for microbial genomes with TriTISA.
Bioinformatics 25,123-125.
:: DESCRIPTION
COLOMBO is a software framework equipped with a GUI for the statistical analysis of sequences of a genome. It can be equipped with different plugins that actually perform the analysis. The current version of COLOMBO is supplied with SIGI-HMM, a tool for the prediction of Genomic Islands.
::DEVELOPER
Theoretical Computer Science and Algorithmic Methods , at the University of Göttingen.
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Score-based prediction of genomic islands in prokaryotic genomes using hidden Markov models.
Waack S, Keller O, Asper R, Brodag T, Damm C, Fricke WF, Surovcik K, Meinicke P, Merkl R.
BMC Bioinformatics. 2006 Mar 16;7:142.
:: DESCRIPTION
PGAAS is prokaryotic genome assembly assistant system. The approach upon which PGAAS is based is to confirm the order of contigs and fill gaps between contigs through peptide links obtained by searching each contig end with BLASTX against protein database.
::DEVELOPER
Center for Bioinformatics, PKU.
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
PGAAS: a prokaryotic genome assembly assistant system.
Yu Z, Li T, Zhao J, Luo J.
Bioinformatics. 2002 May;18(5):661-5.
:: DESCRIPTION
OxyGene is an innovative platform that addresses exploration and comparative analysis of oxidative stress subsystems in prokaryotic whole genomes. OxyGene integrates an original annotation database, called OxyDB, holding thoroughly tested signatures and a new ontology for ab initio detection of ROS/RNS response genes. Data can be downloaded and viewed using an intuitive graphic user-friendly interface that contains tabular, graphical and text tools.
::DEVELOPER
B@SIC (Bioinformatics Applied to Stresses and Cellular Interactions)
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
David Thybert , Stéphane Avner , Céline Lucchetti-Miganeh , Angélique Chéron and Frédérique Barloy-Huble
OxyGene: an innovative platform for investigating oxidative-response genes in whole prokaryotic genomes
BMC Genomics 2008, 9:637
