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Andhra Village Aunty |top| -

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

Andhra Village Aunty |top| -

And when you leave, she will press a mamidi pandu (ripe mango) into your hand and say, “ Malli raa, kodaka ” — Come again, son/daughter. And you will. You always will. Would you like this adapted into a short story, script for a web series, or a social media post series?

In the sun-baked coastal plains and lush delta regions of Andhra Pradesh, amid swaying coconut groves and emerald paddy fields, there exists a figure both unassuming and indispensable: the Andhra village aunty . She is not a single person but a force of nature—everyone’s aunt, no one’s blood relative, yet an unwavering pillar of her community. 1. The First Light Activist Long before the rooster crows, she’s awake. She sweeps the front yard with a cheema chettu (broomstick), draws intricate muggu (kolam/rangoli) with rice flour at the doorstep, and lights the deepam (lamp) inside a tiny, flower-decked shrine. Her day is a quiet ritual of order—a silent prayer for rain, for health, for the village’s well-being. 2. The Unwritten Law of the Gummadi (Pumpkin) Walk into any courtyard, and you’ll find her sitting cross-legged, sorting freshly harvested bendakaya (okra) or peeling sorakaya (bottle gourd). But her real power? She mediates disputes. A boundary issue between two families? The aunty settles it with a stern “ Chalu, chalu (enough, enough)” over a shared cup of gummadi koora (pumpkin curry). Her judgment is never written, but always honored. 3. Culinary Custodian of Royyala Iguru (Prawn Curry) Her kitchen is a temple of pachi pulusu (raw tamarind soup) and avakaya (mango pickle). She knows exactly when the karivepaku (curry leaves) must be added to sizzling mustard seeds, and she alone holds the secret of her mother’s natu kodi pulusu (country chicken curry). When a grand feast is planned—be it a pelli (wedding) or seemanta (baby shower)—she is the general commanding the battalu (ladles). Guests don’t ask who cooked; they simply ask, “Which aunty made this?” 4. The Unpaid Therapist & Matchmaker She listens—without judgment—to the young bride who misses her mother, the old farmer who lost his bullock, the teenager failing math. Her advice is sharp, seasoned with proverbs like: “ Vennela ki vanta chesi, veyi rojulu bratakali ” (Cook with moonlight and live a thousand days). And when a boy and girl from neighboring villages “like” each other? She becomes the silent courier of jasmine flowers —a coded language only village aunties understand. 5. Fashion That Defies Trends Her wardrobe is a practical poetry: a crisp, faded cotton saree (often Mangalagiri or Uppada ), pulled tight, with a pachi tala (raw turmeric) smudge on her forehead. Her feet are bare, toes stained with gorintaku (henna). In her ear hangs a single guchhi (cluster of gold beads) — her only luxury. When she visits town, she might wear a synthetic printed saree ; the moment she returns, she folds it away. “ Pattu ki puli enduku? ” she laughs — Why add silk to a storm? 6. Technology? She’s Not Amused Her smartphone (a hand-me-down from a son in Hyderabad) is used only for two things: watching Devotional songs on YouTube at full volume during bhajans , and video-calling grandchildren who live in “that America.” Her response to WhatsApp forwards? “ Avna? Nizamena? ” (Really? Is it true?) — before deleting them all. 7. The Protector of Traditions When a younger woman suggests wearing jeans to the cheruvu (tank bund), the aunty will raise an eyebrow and deliver her classic line: “ Cheera kattukunte chali tagguddi, kaani jeans valla gunde noppi vasthundi ” (You’ll stay cooler in a saree, jeans give you heart pain). She doesn’t suppress modernity; she simply refuses to be impressed by it. Her silent resistance is more powerful than any speech. 8. A Reservoir of Strength Yet, beneath her formidable exterior lies deep vulnerability. She lost her husband to a tractor accident twenty years ago. She raised three children on ration rice and menthi kura (fenugreek leaves). She never remarried. She never complained. Her tears are shed only when the borewell runs dry or when the paddy sapling fails to take root. That is the weight she carries — the weight of a land that gives and takes. In Conclusion: Why She Matters The Andhra village aunty is not a caricature. She is a living archive of climate knowledge, folk medicine, caste dynamics, and culinary heritage. In an era of rapid urbanization, she is the last anchor of grama jeevana sampradayalu (village life traditions). To spend an afternoon with her — shelling pesarapappu (moong dal) under a mamidi chettu (mango tree) — is to understand that development is not about concrete roads, but about human continuity. andhra village aunty

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)


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