Genome Bioinformatics

Jim Kent’s Source Tree and CVS repository.

UCSC Genome Browser Wiki

Drosophila Genomics

LBNL/UC-Berkeley’s Drosophila Assembly Annotation & Alignment (AAA) Homepage and Wiki.

NHGRI’s Fruitfly Genome Sequencing Homepage.

NCBI’s Drosophila Genome Resources Homepage.

DroSpeGe: Drosophila Species Genomes Homepage.

Drosophila Population Genomics Project (DPGP) Homepage.

Baylor College of Medicine’s Drosophila Genetic Reference Panel (DGRP) Homepage.

Drosophila Polymorphism and Divergence Project Homepage.

Tucson Drosophila Genomics Consortium Homepage.

Riken’s National BioResources Project Drosophila BAC Database.

Drosophila Polymorphism Database.

LBNL’s Drosophila Heterochromatin Genome Project (DHGP) Homepage.

UC-Santa Cruz’s Drosophila Genome Browser.

Ensembl’s Drosophila Genome Browser.

NCBI’s Drosophila Map Viewer.

FlyBase’s Generic Genome Browser.

modENCODE Generic Genome Browser.

Lior Pachter’s Drosophila K-browser

Inna Dubchak’s Drosophila VISTA Genome Browser.

Drosophila Gene Disruption Project Database.

Harvard Exelixis Collection.

Calvin Bridge’s Polytene Maps.

Cavalli Lab Polycomb and Trithorax Page .

Regulatory Bioinformatics

ORegAnno: The Open Regulatory Annotation Database.

PAZAR: A Public Database of Transcription Factor Binding Sites and Regulatory Sequence Annotation.

The REDfly database of Drosophila CRMs and Transcription Factor Binding Sites.

Dmitri Papatsenko’s Homepage.

Drosophila Core Promoter Database.

Thomas Down’s N’MICA package for motif inference and MotifExplorer tool for PWM analysis.

Boris Adryan’s Drosophila Transcription Factor Database.

Maximillian Haussler’s Regulatory Informatics wiki page.

Berkeley Drosophila Transcription Network Project Homepage.

Cavalli Lab ChIP-chip browser.

Pugh Lab nucleosome browser.

BDGP embryonic in situ database.

Krause Lab Fly-FISH database.

FlyExpress expression pattern search engine.

Openflydata cross-database search tools

NESCent, The National Center for Evolutionary Synthesis.

NESCent Working Group on cis-regulatory molecular evolution.

The RegCreative Jamboree.

Text Mining

NACTEM, the National Centre for Text Mining.

The BioCreAtIvE text mining challenge.

GIFT, a gene interaction finder in text.

iHOP, a gene network for navigating the biomedical literature.

Highwire Press’s Full Text Search page.

PubMedCentral’s Digital Archive.

HubMed, an alternative interface to PubMed.

Google Scholar.

ISI’s Web of Knowledge.

eTBLAST, a textual similarity search engine.

JANE, the Journal/Author Name Estimator.

BioText Search Engine.

YIF, Yale Image Finder.


UW-Milwaukee Biomedical Figure Search.





Genome Rearangement

Matthieu Blanchette’s BPanalysis.

Bernard Moret et al.’s Grappa.

Klaas Vandepole et al’s Automatic Detection of Homologous Regions (ADHoRe)

Ying Lin et al’s Sorting Permutation by Reversals and block-INterchanGes (SPRING)

Glenn Tesler’s Genome Rearrangements in Mouse and Man (GRIMM).

Guillaume Borque’s Multiple Genome Rearrangements (MGR).

Bret Larget’s Bayesian Analysis to Describe Genomic Evolution by Rearrangement (BADGER)

A.J. Bukhtar’s Neighboring Gene Pair Neighboring Gene Pairs (NGP).

Simon Gog et al.’s Genome evolution scenarios (GENESIS).

Claire Lemaitre’s Cassis.

Firas Swidan’s MAGIC.

Aaron Darling’s MAUVE.

Sinha and Meller’s Cinteny

Transposable elements and Repetitive DNA

Genetic Information Research Institute’s Repbase.

Hadi Quesneville’s REPET database.

Wojciech Makalowski’s Genomic Scrapyard Database

Jurgen Brosius’ Tables of Retronuons.

Douda Bensasson’s Table of NUMTS.

An up-to-date version of Table 1 from Bergman and Quesneville (2007) “Discovering and detecting transposable elements in genome sequences” is available here.

Network Tools

Cytoscape, a tool for visualizing molecular interactions.

BioLayout, An automatic graph layout algorithm for similarity and network visualization.

GraphViz, graph vizualization software.

BioTapestry, a tool for building, visualizing, and simulating genetic regulatory networks.

CPAN Graph module.


YouTube clips of Michael Ashburner discussing open-access publishing [1, 2, 3].

Charlie Rose interviews on Human Genomics.

How transposons really work.

The Software Sustainability Institute.

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