The Shocking Details of Genome.ucsc.edu. History of the Code. Started in 1999 in C after Java proved hopelessly unportable across browsers. Early modules include a Worm genome browser (Intronerator), and GigAssembler which produced working draft of human genome.
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The Shocking Details of Genome.ucsc.edu
Make the human genome
understandable by humans.
Maybe we’ll understand it one of these days
#chrom start end [name strand score …]
chr1 1302347 1302357 SP1 + 800
chr1 1504778 1504787 SP2 – 980
/* A dna sequence in one-letter-per-base format. */
struct dnaSeq *next; /* Next in list. */
char *name; /* Sequence name. */
char *dna; /* a’s c’s g’s and t’s. Null terminated */
int size; /* Number of bases. */
struct dnaSeq *dnaSeqFromString(char *string);
/* Convert string containing sequence and possibly
* white space and numbers to a dnaSeq. */
void dnaSeqFree(struct dnaSeq **pSeq);
/* Free dnaSeq and set pointer to NULL. */
void dnaSeqFreeList(struct dnaSeq **pList);
/* Free list of dnaSeq’s. */
/* A two dimensional object in a sleazy video game. */
struct screenObj *next; /* Next in list. */
char *name; /* Object name. */
int x,y,width,height; /* Bounds of object. */
void (*draw)(struct screenObj *obj); /* Draw object */
boolean (*in)(struct screenObj *obj, int x, int y);
/* Return true if x,y is in object */
void *custom; /* Custom data for a particular type */
void (*freeCustom)(struct screenObj *obj);
/* Free custom data. */
#define screenObjDraw(obj) (obj->draw(obj))
/* Draw object. */
void screenObjFree(struct screenObj **pObj);
/* Free up screen object including custom part. */
struct exoFish *exoFishLoad(char **row)
/* Load a exoFish from row fetched with select * from exoFish
* from database. Dispose of this with exoFishFree(). */
struct exoFish *ret;
ret->chrom = cloneString(row);
ret->chromStart = sqlUnsigned(row);
ret->chromEnd = sqlUnsigned(row);
ret->name = cloneString(row);
ret->score = sqlUnsigned(row);
"An evolutionarily conserved region (ecore) with Tetroadon"
string chrom; "Human chromosome or FPC contig"
uint chromStart; "Start position in chromosome"
uint chromEnd; "End position in chromosome"
string name; "Ecore name in Genoscope database"
uint score; "Score from 0 to 1000"
See autoSql.doc for more details.
See also autoXml
Expression and other information on genes in a big sorted, linked table