Tag: Genome

PHIRE 1.00 – Reveal Regulatory Elements in Bacteriophage Genomes

PHIRE 1.00

:: DESCRIPTION

PHIRE (PHage In silico Regulatory Elements) is a standalone program in Visual Basic, performs an algorithmic string-based search on bacteriophage genome sequences, discovering and extracting blocks displaying sequence similarity, corresponding to conserved regulatory elements contained within these genomes in a systematic manner, without any prior experimental or predictive knowledge.

::DEVELOPER

Lighthouse data

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

PHIRE

:: MORE INFORMATION

Citation

Lavigne, R., Sun, W.D. and Volckaert, G.
PHIRE, a deterministic approach to reveal regulatory elements in bacteriophage genomes.
Bioinformatics (2004) 20: 629-635.

Ebbie-MM 4.3 – Analyze Single Mismatches of Small RNAs to the genome

Ebbie-MM 4.3

:: DESCRIPTION

Ebbie-MM (Ebbie-(mis)match) is a software that analyzes single mismatches of small RNAs to the genome of origin. Using Ebbie-MM, we analyzed a dataset of 7,790 non-redundant small RNAs cloned from Oryza sativa. In this limited dataset, we found 230 1-nt-mismatches of which only 19 % overlapped to themselves. Even with this very limited dataset of 43 overlapping 1-nt-mismatches, RNA base modifications were detectable in small RNAs. Thus, not all sequencing errors should be discarded as they could contain valuable information on RNA base modifications.

::DEVELOPER

H Alexander Ebhardt , Herbert H. Tsang and Denny C. Dai .

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / MacOsX / Linux
  • Java
  • NCBI-Blast

:: DOWNLOAD

Ebbie-MM

:: MORE INFORMATION

Citation

H. Alexander Ebhardt, Herbert H. Tsang, Denny C. Dai, Yifeng Liu, Babak Bosta3 and Richard P. Fahlman
Meta-analysis of small RNA-sequencing errors reveals ubiquitous post-transcriptional RNA modifications
Nucl. Acids Res. (2009) 37 (8): 2461-2470

GenomePixelizer 2003.10.1 – Genome Visualization Tool

GenomePixelizer 2003.10.1

:: DESCRIPTION

GenomePixelizer is a visualization tool that generates custom images of the physical or genetic positions of specified sets of genes in whole genomes or parts of genomes. Multiple sets of genes can be shown simultaneously with user-defined characteristics displayed. It allows the analysis of duplication events within and between species based on sequence similarities. GenomePixelizer may be useful in the detection of duplication events in genomes, tracking the “footprints” of evolution, as well as displaying the genetic maps and other aspects of comparative genetics.

GenomePixelizer may be considered a drawing tool that generates custom images of genomes out of the given set of genes. Each element on the picture has a physical address defined by coordinates (pixels), hence the name “GenomePixelizer”.

::DEVELOPER

GenomePixelizer Team, University of California

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Mac / Linux
  • Tcl/Tk

:: DOWNLOAD

GenomePixelizer

:: MORE INFORMATION

Citation

A. Kozik, E. Kochetkova and R. Michelmore
GenomePixelizer—a visualization program for comparative genomics within and between species
Bioinformatics (2002) 18 (2): 335-336.

Metal 20110325 – Meta-analysis of Genomewide Association Scans

Metal 20110325

:: DESCRIPTION

Metal (Meta Analysis Helper) is designed to facilitate meta-analysis of large datasets (such as several whole genome scans) in a convenient, rapid and memory efficient manner.

::DEVELOPER

Abecasis Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Mac /  Linux

:: DOWNLOAD

Metal

:: MORE INFORMATION

Citation:

Cristen J. Willer, Yun Li and Gonçalo R. Abecasis
METAL: fast and efficient meta-analysis of genomewide association scans
Bioinformatics (2010) 26 (17): 2190-2191.

If you decide to use Metal, please take a minute to register.

SeedMasker – Genome Masking based on High Occurrence Words

SeedMasker

:: DESCRIPTION

SeedMasker is public domain software for masking genomes based on over-represented words.

::DEVELOPER

Robert Edgar

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

SeedMasker

:: MORE INFORMATION

Citation

For now, please cite this URL:

http://www.drive5.com/seedmasker

 

Base-By-Base – Genome Pairwise & Multiple Alignment Editor

Base-By-Base

:: DESCRIPTION

Base-By-Base is a whole genome pairwise and multiple alignment editor. The program highlights differences between pairs of alignments and allows the user to easily navigate large alignments of similar sequences. Although Base-By-Base was intended as an editor and viewer for alignments of highly similar sequences, it is also provides many of the functions of other generic alignment editors.

::DEVELOPER

Dr. Chris Upton, University of Victoria, Biochemistry and Microbiology

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Java

:: DOWNLOAD

Base-By-Base

:: MORE INFORMATION

Citation:

Brodie, R., A.J. Smith, R.L. Roper, V. Tcherepanov, and C. Upton. 2004.
Base-By-Base: Single nucleotide-level analysis of whole viral genome alignments, BMC Bioinformatics, 5, 96.

 

VariantClassifier 20100603 – Hierarchical Variant Classifier for Annotated Genomes

VariantClassifier 20100603

:: DESCRIPTION

VariantClassifier is a software tool for hierarchically classifying variants based on the genome annotation that is provided.  Instead of looking at a region of the genome and seeing all the features relative to each other on the genomic axis, the VariantClassifier inverts the process so that novel variants can be tested for interest, based on the known features on the genomic axis.  Furthermore, our hierarchical classification provides a prioritization of the variants that should be considered for more intensive study.

::DEVELOPER

J. Craig Venter Institute

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

VariantClassifier

:: MORE INFORMATION

Citation:

Kelvin Li and Timothy B Stockwell
VariantClassifier: A hierarchical variant classifier for annotated genomes
BMC Research Notes 2010, 3:191doi:10.1186/1756-0500-3-191

HMDFinder – Methylation Prediction in Human Genome

HMDFinder

:: DESCRIPTION

HMDFinder is a software of Methylation prediction in human genome. HMDFinder has a prediction accuracy of 86%, as validated with CpGs regions for which methylation status have been experimentally determined. Using HDMFinder, we are able to depict the entire genomic methylation patterns for all 22 human autosomes.

::DEVELOPER

Zhang Lab, Cold Spring Harbor Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

HMDFinder

:: MORE INFORMATION

PNAS in press

Computational Prediction of DNA Methylation Landscape in the Human Genome

Rajdeep Das , Nevenka Dimitrova , Zhenyu  Xuan, Robert A. Rollins , Fatemah G. Haghighi , John R. Edwards , Jingyue Ju , Timothy H. Bestor  and Michael Q. Zhang

LuceGene 1.4 – Search System for Genome & Bioinformatic Databases

LuceGene 1.4

:: DESCRIPTION

LuceGene is an open-source document/object search and retrieval system specially tuned for bioinformatics text databases and documents. LuceGene is similar in concept to the widely used, commercially successful, bioinformatics program SRS (Sequence Retrieval System).

LuceGene is speedy with big data sets: Searching the UniProt library of 1.7 million sequences with LuceGene is a close equivalent to SRS in speed and content. Gene Annotation object search and retrieval with LuceGene is 10x to 20x faster than using a Postgres Chado database. LuceGene has been tested and works well with millions of documents from genome sequence, annotation and literature databases.

LuceGene Demo Web Version

::DEVELOPER

D. Gilbert,Paul Poole (pppoole@bio.indiana.edu), Etc.

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

LuceGene

:: MORE INFORMATION

Contactemail:  lucegene AT eugenes.org

Flash GViewer 0.5 – Customizable Flash Movie to Display Chromosome in Genome

Flash GViewer 0.5

:: DESCRIPTION

Flash GViewer is a customizable Flash movie that can be easily inserted into a web page to display each chromosome in a genome along with the locations of individual features on the chromosomes. It is intended to provide an overview of the genomic locations of a specific set of features – eg. genes associated with a specific ontology term, etc., rather than as a way to view all features on the genome. The features can hyperlink out to a detail page to enable to GViewer to be used as a navigation tool. Genome maps for Rat, Mouse, Human and C. elegans are provided but other genome maps can be easily created. Annotation data can be provided as static text files or produced as XML via server scripts.

::DEVELOPER

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

Flash GViewer

:: MORE INFORMATION

Contact:  Simon Twigger

 

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