:: DESCRIPTION
eGATU (easy Genome Annotation Transfer Utility) is a light application modelled on GATU. It allows users to transfer annotations to an input genome without having to specify a reference.
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:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
GFS (Genome-based fingerprint scanning) is a program that maps peptide mass fingerprint data directly to raw genomic sequence, enabling rapid, low-cost identification of proteins in genomes for which annotation is lacking. An experimentally obtained peptide mass fingerprint is entered into the program, which then scans a genome sequence of interest, and outputs the most likely regions of the genome from which the mass fingerprint is derived.
The Upton lab developed this JAVA interface to GFS and is grateful to the Giddings lab for access to the software and their help.
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:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Giddings MC, Shah AA, Gesteland R and Moore B (2003)
Genome-based peptide fingerprint scanning.
Proc Natl Acad Sci USA. 100:20-5
:: DESCRIPTION
GATU (Genome Annotation Transfer Utility) annotates a genome based on a very closely related reference genome. The proteins/mature peptides of the reference genome are BLASTed against the genome to be annotated in order to find the genes/mature peptides in the genome to be annotated.
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:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Tcherepanov, T., Ehlers, A. and Upton, C. 2006.
Genome Annotation Transfer Utility (GATU): Rapid annotation of viral genomes using a closely related reference genome. BMC Genomics 7:150.
:: DESCRIPTION
Codon Statistics (CS) is a java based user interface, which enables one to quickly browse statistical information on one or more genomes. One may view statistical information on both graphical and tabular forms.
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:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
MyRAST (Rapid Annotations using Subsystems Technology) is a software for the RAST Server, a fully automated annotation service for complete, or near-complete, archaeal and bacterial genomes.
::DEVELOPER
The SEED framework for comparative genomics
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:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Ramy K Aziz, etc.
The RAST Server: Rapid Annotations using Subsystems Technology
BMC Genomics. 2008; 9: 75.
:: DESCRIPTION
GEB is a Java application developed to provide a dynamic graphical interface to visualise the distribution of genome features and chromosome-wide experimental data in high resolution.
::DEVELOPER
the Bioinformatics Support Service, Centre for Bioinformatics, Imperial College London, UK and the MRC Clinical Sciences Centre, London, UK
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:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
BMC Bioinformatics. 2008 Nov 27;9:501. doi: 10.1186/1471-2105-9-501.
Genome Environment Browser (GEB): a dynamic browser for visualising high-throughput experimental data in the context of genome features.
Huntley D, Tang YA, Nesterova TB, Butcher S, Brockdorff N.
:: DESCRIPTION
FR-HIT is a Very Fast Program to Recruit Metagenomic Reads to Homologous Reference Genomes.Fragment recruitment, a process of aligning sequencing reads to reference genomes, is a crucial step in metagenomic data analysis. The available sequence alignment programs are either slow or insufficient for recruiting metagenomic reads. We implemented an efficient algorithm, FR-HIT, for fragment recruitment. We applied FR-HIT and several other tools including BLASTN, MegaBLAST, BLAT, LAST, SSAHA2, SOAP2, BWA and BWA-SW to recruit 4 metagenomic datasets from different type of sequencers. On average, FR-HIT and BLASTN recruited significantly more reads than other programs, FR-HIT is about 2 orders of magnitude faster than BLASTN. FR-HIT is slower than the fastest SOAP2, BWA and BWA-SW, but it recruited 1-5 times more reads.
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N/A
:: REQUIREMENTS
:: MORE INFORMATION
Citation
Beifang Niu, Zhengwei Zhu, Limin Fu, Sitao Wu, Weizhong Li.
FR-HIT, a Very Fast Program to Recruit Metagenomic Reads to Homologous Reference Genomes.
Bioinformatics. (2011) 27 (12): 1704-1705. doi: 10.1093/bioinformatics/btr252
:: DESCRIPTION
GRS is a novel compression tool for storing and analyzing Genome ReSequencing data. GRS is able to process the genome sequence data without the use of the reference SNPs and other sequence variation information and automatically rebuild the individual genome sequence data using the reference genome sequence.
:: DEVELOPER
Congmao Wang, Shanghai Jiao Tong University plant developmental biology laboratory.
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Nucleic Acids Res. 2011 Apr;39(7):e45. doi: 10.1093/nar/gkr009. Epub 2011 Jan 25.
A novel compression tool for efficient storage of genome resequencing data.
Wang C, Zhang D.
:: DESCRIPTION
The ECR Browser is a dynamic graphical interface that allows users to visualize and analyze Evolutionary Conserved Regions (ECRs) in genomes of sequenced species.
::DEVELOPER
Ivan Ovcharenko Research Group
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:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
ECR Browser: a tool for visualizing and accessing data from comparisons of multiple vertebrate genomes.
Ovcharenko I, Nobrega MA, Loots GG, Stubbs L.
Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W280-6.
:: DESCRIPTION
Curtain is an assembler of next generation sequence. Curtain is a Java wrapper around next-generation assemblers such as Velvet, which allows the incremental introduction of read-pair information into the assembly process.
::DEVELOPER
Matthias Haimel, email: mhaimel.ebi@googlemail.com
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION