double seqTm(char *seq, double dna_conc, double salt_conc)
/* Figure out melting temperature of sequence of any length given
* dna and salt concentration. */
{
int len = strlen(seq);
return (len > 36)
? longSeqTm(seq, 0, len, salt_conc) : oligoTm(seq, dna_conc, salt_conc);
}
boolean doPcr(struct pcrServer *server, struct targetPcrServer *targetServer,
char *fPrimer, char *rPrimer,
int maxSize, int minPerfect, int minGood, boolean flipReverse)
/* Do the PCR, and show results. */
{
struct errCatch *errCatch = errCatchNew();
boolean ok = FALSE;
hgBotDelay();
if (flipReverse)
reverseComplement(rPrimer, strlen(rPrimer));
if (errCatchStart(errCatch))
{
struct gfPcrInput *gpi;
AllocVar(gpi);
gpi->fPrimer = fPrimer;
gpi->rPrimer = rPrimer;
if (server != NULL)
doQuery(server, gpi, maxSize, minPerfect, minGood);
if (targetServer != NULL)
doTargetQuery(targetServer, gpi, maxSize, minPerfect, minGood);
ok = TRUE;
}
errCatchEnd(errCatch);
if (errCatch->gotError)
warn("%s", errCatch->message->string);
errCatchFree(&errCatch);
if (flipReverse)
reverseComplement(rPrimer, strlen(rPrimer));
webNewSection("Primer Melting Temperatures");
printf("<TT>");
printf("<B>Forward:</B> %4.1f C %s<BR>\n", oligoTm(fPrimer, 50.0, 50.0), fPrimer);
printf("<B>Reverse:</B> %4.1f C %s<BR>\n", oligoTm(rPrimer, 50.0, 50.0), rPrimer);
printf("</TT>");
printf("The temperature calculations are done assuming 50 mM salt and 50 nM annealing "
"oligo concentration. The code to calculate the melting temp comes from "
"<A HREF=\"http://frodo.wi.mit.edu/primer3/input.htm\" target=_blank>"
"Primer3</A>.");
return ok;
}
