Category: DNA / Genome Analysis

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

 

CMap 1.01 – View Comparisons of Genetic & Physical Maps

CMap 1.01

:: DESCRIPTION

CMap (omparative Map Viewer) is a web-based tool that allows users to view comparisons of genetic and physical maps. The package also includes tools for curating map data. A user can compare an unlimited number of maps, view pair-wise comparisons of known correspondences, and search for maps or for features by name, species, type and accession. CMap is freely available, can run on a variety of database engines and uses only free and open software components.

::DEVELOPER

the Generic Model Organism Database

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Mac OsX / Linux /
  • Perl 5.6.0 or higher
  • web server with CGI capabilites (e.g., Apache 1.x or 2.x)
  • A relational database, e.g. MySQL (4.0+), Sybase Adaptive Server Enterprise, PostgreSQL, SQLite or Oracle (9.x)
  • libgd 2.0.28 and GD.pm 2.15
  • Various Perl modules available on CPAN

:: DOWNLOAD

CMap ;  Documation

:: MORE INFORMATION

Citation

Ken Youens-Clark, Ben Faga, Immanuel V. Yap, Lincoln Stein and Doreen Ware
CMap 1.01: a comparative mapping application for the Internet.
, Bioinformatics 2009 25(22):3040-3042; doi:10.1093/bioinformatics/btp458.

blastGraphic 0.02 – BLAST Graphic Viewer

blastGraphic 0.02

:: DESCRIPTION

blastGraphic (BLAST Graphic Viewer)  provides a graphical visualization of the regions contained within HSPs relative to the query sequence.This graphic module will support BLASTN, BLASTP, BLASTX, TBLASTX,    TBLASTN, BLAT, and TBLATN. For the databases, it will support any fasta-   formated datasets (i.e., nr, nt, etc).

::DEVELOPER

Shuai Weng & SGD team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

blastGraphic

:: MORE INFORMATION

blastGraphic is a free software. You can use it under the same terms as Perlitself.

 

FootPrinter 2.1 / MicroFootPrinter – Phylogenetic Footprinting

FootPrinter 2.1

:: DESCRIPTION

FootPrinter is a program for phylogenetic footprinting. Phylogenetic footprinting is a method that identifies putative regulatory elements in DNA sequences. It identifies regions of DNA that are unusually well conserved across a set of orthologous sequences.

FootPrinter Web version

MicroFootPrinter is a front end to the FootPrinter phylogenetic footprinting program, but with specific focus on prokaryotic genomes. You supply a prokaryotic species and gene of interest, and you set a few parameters (or leave them at their default values). MicroFootPrinter will then find related prokaryotes containing a homologous gene, and run FootPrinter to identify motifs that are well conserved across the cis-regulatory regions of these homologous genes.

MicroFootPrinter Web Version

::DEVELOPER

The Computational & Synthetic Biology group – COMPUTER SCIENCE & ENGINEERING at UNIVERSITY OF WASHINGTON

:: SCREENSHOTS

FootPrinter

MicroFootPrinter

:: REQUIREMENTS

:: DOWNLOAD

FootPrinter Source Code ; Manual

:: MORE INFORMATION

Citation for FootPrinter:

  • M. Blanchette, B. Schwikowski, M. Tompa, “Algorithms for phylogenetic footprinting”, J. Comput. Biol., vol. 9 (2002) 211-23. Pubmed 12015878.
  • M. Blanchette, M. Tompa, “Discovery of regulatory elements by a computational method for phylogenetic footprinting”, Genome Res., vol. 12 (2002) 739-48.Pubmed 11997340.   Supplement.
  • M. Blanchette, M. Tompa, “FootPrinter: A program designed for phylogenetic footprinting”, Nucleic Acids Res., vol. 31 (2003) 3840-2. Pubmed 12824433.

Citation for MicroFootPrinter:

PGT 0.42 – Projection Genomics Toolkit

PGT 0.42

:: DESCRIPTION

PGT (Projection Genomics Toolkit) is a software to Find motifs using random projections.

::DEVELOPER

Jeremy Buhler

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

PGT source code (C++)

:: MORE INFORMATION

Citation

  • J. Buhler. “Efficient large-scale sequence comparison by locality-sensitive hashing.” Bioinformatics 17:419-429, 2001.
  • J. Buhler and M. Tompa. “Finding motifs using random projections.” Journal of Computational Biology 9(2):225-242, 2002. (An earlier version of this work appeared at ACM RECOMB 2001.)
  • J. Buhler. “Provably sensitive indexing strategies for biosequence similarity search.” Journal of Computational Biology 10(3/4):399-418, 2003. (An earlier version of this work appeared at ACM RECOMB 2002.)

    • MSS 1.0 – Finding all Maximal Scoring Subsequences

    MSS 1.0

    :: DESCRIPTION

    MSS (Maximal Scoring Subsequences) is a practical, linear time algorithm to find, in a sequence of numeric scores, those nonoverlapping, contiguous subsequences having greatest total scores.

    ::DEVELOPER

    The Computational & Synthetic Biology group – COMPUTER SCIENCE & ENGINEERING at UNIVERSITY OF WASHINGTON

    :: SCREENSHOTS

    Command Line

    :: REQUIREMENTS

    :: DOWNLOAD

    MSS Source Code

    :: MORE INFORMATION

    Citation:

    W. Ruzzo, M. Tompa, “A linear time algorithm for finding all maximal scoring subsequences”, Proc Int Conf Intell Syst Mol Biol, (1999) 234-41. Pubmed 10786306.

     

    paircomp 1.0 – Ungapped Comparisons of Two Sequences

    paircomp 1.0

    :: DESCRIPTION

    paircomp is a toolkit for doing ungapped comparisons of two DNA sequences. It contains a C++ library, several standalone command-line programs, and a Python interface to the C++ library.

    ::DEVELOPER

    C. Titus Brown

    :: SCREENSHOTS

    Command Line

    :: REQUIREMENTS

    • Windows / Mac OsX / Linux
    • python

    :: DOWNLOAD

    paircomp

    :: MORE INFORMATION

    Citation:

    Paircomp, FamilyRelationsII and Cartwheel: tools for interspecific sequence comparison
    Brown CT, Xie Y, Davidson EH, and Cameron RA.
    BMC Bioinformatics 2005, 6:70. 24 Mar 2005

    FamilyRelations II 20070330 – Comparative Sequence Analysis

    FamilyRelations II 20070330

    :: DESCRIPTION

    FamilyRelations II (henceforth, “FR II”) is a program which lets you visually explore the results of various analyses; it’s what you use once you’ve set up an analysis and want to see the results.

    ::DEVELOPER

    C. Titus Brown

    :: SCREENSHOTS

    :: REQUIREMENTS

    • Windows / Mac OsX / Linux
    • JAVA

    :: DOWNLOAD

    FamilyRelations II

    :: MORE INFORMATION

    Citation:

    Paircomp, FamilyRelationsII and Cartwheel: tools for interspecific sequence comparison
    Brown CT, Xie Y, Davidson EH, and Cameron RA.
    BMC Bioinformatics 2005, 6:70. 24 Mar 2005