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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/signal__seq_8cpp_source.html below:

NCBI C++ ToolKit: src/algo/sequence/signal_seq.cpp Source File

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{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}

186 template

class

Seq>

191 if

(seq.size() < 15) {

192 throw

runtime_error(

"Sequence length must be at least 15 " 193 "to predict signal sequence"

);

196 throw

runtime_error(

"max_pos must be at least 12 " 197 "to predict signal sequence"

);

200 const

double (*Mat)[15];

209 double

max_score = -1e6;

211 for

(

unsigned int i

= 0;

<= max_index;

++) {

213 for

(

unsigned int

j = 0; j < 15; j++) {

214 int

sub = (

unsigned

char)seq[

+ j];

217 if

(sum > max_score) {

244 string

seq_ncbistdaa;

247

vec.GetSeqData(0, vec.size(), seq_ncbistdaa);

friend void x_PredictSignalSeq(const Seq &seq, CSignalSeq::EDomain domain, TSeqPos max_pos, TSeqPos &pos, double &score)

static void Predict(const string &seq, EDomain domain, TSeqPos max_pos, TSeqPos &pos, double &score)

Find the most likely predicted signal sequence cleavage site (pos) and the associated score (>3....

unsigned int TSeqPos

Type for sequence locations and lengths.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

void x_PredictSignalSeq(const Seq &seq, CSignalSeq::EDomain domain, TSeqPos max_pos, TSeqPos &pos, double &score)

const double const_BacMat[26][15]

const double const_EukMat[26][15]

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