Eucaryote용 GenePrediction 프로그램으로, [[Gene]]의 exon-intron structure와 location을 예측해 준다.

http://genes.mit.edu/GENSCAN.html

[[Protein]]코딩영역만을 예측해준다. 따라서, r[[RNA]], t[[RNA]]등은 다른 프로그램을 이용해야한다.

본 프로그램만을 이용하여 만들어진 서열을 [[Protein]] [[Translation]]한 서열데이터베이스가 TrGen이다.

SeeAlso EstScan

----
GenScan 결과의 [[Parsing]]
{{{#!python
"""This parser is working when using "-v -cds" options"""
class GenscanReport:
    def __init__(self):
        self.genes = list()
    def addGene(self, gene):
        self.genes.append(gene)

class Gene:
    def __init__(self, no):
        self.no = no
        self.exons = list()
        self.cds = ''
        self.peptide = ''
    def addExon(self, exon):
        self.exons.append(exon)

    def setCds(self, fasta):
        self.cds = fasta
    def setPeptide(self, fasta):
        self.peptide = fasta

class Exon:
    def __init__(self, no, type, strand, begin, end):
        self.no = no
        self.type = type
        self.strand = strand
        self.begin = int(begin)
        self.end = int(end)

class FastaIterator:
    def __init__(self, ifile):
        self.ifile = ifile
        self.g = self.getGenerator()
    def getGenerator(self):
        while True:
            line = self.ifile.next().strip()
            if line:
                lines = [line+'\n']
                break
        for line in self.ifile:
            if line.startswith('Explanation'):
                yield ''.join(lines)
                break
            if line.startswith('>'):
                yield ''.join(lines)
                lines = [line]
            else:
                lines.append(line)

    def __iter__(self):
        return self.g

    def next(self):
        return self.g.next()

def parseGenscan(handler):
    gr = GenscanReport()
    while True:
        line = handler.next()
        if line.startswith('-') or line is None: break
    i = 0
    gene = None
    for line in handler:
        line = line.strip()
        if line.startswith('P') or line.startswith('S') or line.startswith('NO'): 
            break
        if not line:
            if gene and gene.exons: gr.addGene(gene)
            i+=1
            gene = Gene(i)
            continue
        words=line.split()
        gene.addExon(Exon(words[0], words[1], words[2], words[3], words[4]))

    while True:
        line = handler.next()
        if line.startswith('Predicted coding') or line is None: break

    fi = FastaIterator(handler)
    for gene in gr.genes:
        gene.setPeptide(fi.next())
        gene.setCds(fi.next())
    return gr

}}}

----
CategoryProgramBio