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Software for motif discovery and next generation sequencing analysis



HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and ChIP-Seq analysis. It is a collection of command line programs for unix-style operating systems written in mostly perl and c++. Homer was primarily written as a de novo motif discovery algorithm that is well suited for finding 8-12 bp motifs in large scale genomics data.

Hardware Requirements (recommended): 2+ Gb memory (4-8+ Gb), 10+ Gb Hard Drive space (50+ Gb)
Software Requirements: Unix compatible OS (or cygwin), perl, gcc, make, wget (optional for full functionality: R, DESeq2, blat, bedGraphToBigWig, liftOver)
License: GPLv3

HOMER works on pretty much any Linux/UNIX systems, including MacOS (if Xcode compilers are installed) and on Windows using either cygwin or a Linux subsystem.

If you are looking specifically for HOMER2, you are in the right place! HOMER2 is integrated into HOMER.

Full Program Download

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Legislative attacks in the United States and abroad have specifically targeted transgender youth (bans on sports participation, puberty blockers, and classroom discussion of gender identity). In response, the LGBTQ community has largely mobilized as a whole . Pride parades that once sidelined trans issues are now led by trans marchers. The term "LGBTQ+" is legally recognized, and the fight for trans healthcare has replaced gay marriage as the civil rights issue of the decade.

However, internal friction remains. Debates over the inclusion of "MAPs" (Minor-Attracted Persons) or the role of kink at Pride are often used by bad-faith actors to fracture the coalition. But the core alliance holds because of a shared lived experience: the experience of being told you are wrong for existing, and the radical act of loving yourself anyway. It is crucial to note that LGBTQ culture is not solely defined by trauma. Within the transgender community, joy is a revolutionary act. Trans joy—seen in TikTok transitions, queer prom nights, and the growing acceptance of neopronouns—is reshaping LGBTQ culture into something more expansive. The binary of "man/woman" is being softened; lesbian spaces are redefining what attraction means; and gay culture is finally reckoning with its own transmisogyny. The Road Ahead: Solidarity as Survival The future of LGBTQ culture depends entirely on the full liberation of the transgender community. We have seen this script before: in the 1980s, when the government ignored the AIDS crisis, the mainstream turned its back on gay men. It was radical queers, trans sex workers, and lesbians who built the harm reduction networks. Today, as anti-trans legislation sweeps across school boards and statehouses, the broader LGBTQ community is returning the favor. shemale trans angels jessy dubai get cleanavi free

For a time in the 1990s and early 2000s, some gay and lesbian organizations tried to "drop the T," arguing that trans issues were separate and risked complicating the fight for marriage equality. This push for assimilation was met with fierce resistance from within. Activists argued that you cannot fight for the right to be gay without fighting for the right to be trans, because both are rooted in the fundamental liberation from assigned roles at birth. Legislative attacks in the United States and abroad

As the rainbow flag continues to wave, its stripes hold a thousand stories. But the light blue, pink, and white of the Transgender Pride Flag—designed by trans woman Monica Helms in 1999—has become an essential horizon line for that rainbow. Without it, the spectrum is incomplete. Without the T, the LGBTQ community is not a community at all, but merely a collection of interests. In the fight for authenticity, safety, and love, the transgender community leads the way—and the rest of us follow. The term "LGBTQ+" is legally recognized, and the

While mainstream narratives often highlight gay men and lesbians, the boots on the ground—the ones who fought back against relentless police brutality—were predominantly trans women, drag queens, and sex workers. Names like (a self-identified transvestite and gay liberation activist) and Sylvia Rivera (a fierce Venezuelan-Puerto Rican trans woman) are no longer footnotes; they are finally being recognized as the matriarchs of the modern LGBTQ rights movement.

Rivera’s famous cry, "It was a riot led by transsexuals—not gay boys, not gay girls—but transsexuals," underscores a difficult truth: The "T" in LGBTQ was not a later addition; it was a founding member. However, for decades after Stonewall, the mainstream gay rights movement, eager to gain social acceptance, often marginalized the very people who threw the first bricks. This tension—between respectability politics and radical authenticity—has defined the relationship between the transgender community and the broader gay/lesbian mainstream. The LGBTQ+ coalition is a strategic alliance, not a monolith. While a gay man and a trans woman both face persecution for defying cis-heteronormativity, their specific oppressions manifest differently.

Program Components and Older Versions

homer2 program - key executable for HOMER motif discovery (homerCppOnly.*.zip). (This archive actually contains all of the c++ executable, not just homer2).  Unzip in the desired directory and simply type "make" to compile the program.

The configuration script really doesn't deal with older versions, but you can download older versions yourself should you really feel like using inferior data or software!
Old Versions of HOMER Software
Old Versions of Organism Packages
Old Versions of Promoter Packages
Old Versions of Genome Packages

Update Information

Change Log - Short description of recent changes

update.txt - Current HOMER configuration list (Currently support human hg17/hg18/hg19, mouse mm8/mm9, rat rn4, X. tropicalis xenTro2, drosophila dm3, and C. elegans ce6, Zebrafish danRer7, yeast sacCer2, Arabidopsis tair10, Rice msu6, Pombe ASM294v1)


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Can't figure something out? Questions, comments, concerns, or other feedback:
cbenner@ucsd.edu