MATLAB中gag,华侨大学课件系列：matlab(生物信息学学习).pdf

华侨大学课件系列：matlab(生物信息学学习)

Matlab生物信息学工具包

Bioinformatics

MatLab Bioinformatics Toolbox

(1)Data Formats and Databases

①getgenbank和genbankread

例1：S = getgenbank('M10051')

返回：S =

例2 ：mitochondria =

getgenbank('NC_001807','SequenceOnly',true)

返回：

mitochondria =

gatcacaggtctatcaccctattaaccactcacgggagctctccatgcat

ttggtattttcgtctggggggtgtgcacgcgatagcattgcgagacgctg

gagccggagcaccctatgtcgcagtatctgtctttgattcctgcctcatt

ctattatttatcgcacctacgttcaatattacaggcgaacatacctacta

aagt . . .

例：getgenbank('nm_000520', 'ToFile',

'TaySachs_Gene.txt')

s = genbankread('TaySachs_Gene.txt')

返回：s=

LocusName:"NM_000520'

LocusSequenceLength:'2255'

LocusNumberofStrands:''

LocusTopology:'linear'

LocusMoleculeType:'mRNA'

LocusGenBankDivision:'PRI'

LocusModificationDate:'23-SEP-2005'

………………

例1：

seq = getgenbank('NM_000546')

codingSeq = seq.Sequence(203:1384)

fastawrite('p53coding.txt','Coding region for p53',codingSeq);

例2 ：p53nt = fastaread('p53coding.txt')

例3 ：Save multiple sequences.

data(1).Sequence = 'ACACAGGAAA'

data(1).Header = 'First sequence'

data(2).Sequence = 'ACGTCAGGTC'

data(2).Header = 'Second sequence'

fastawrite('my_sequences.txt', data)

type('my_sequences.txt')

(2)Sequence Conversion

①aa2nt 和nt2aa

②nt2int 和int2nt ;aa2int 和int2aa

③dna2rna 和rna2dna

④baselookup 和aminolookup

⑤seqcomplement

⑥seqreverse

⑦seqrcomplement

MatLab生物信息学平台统计的函数

1.basecount(count nucleotides in a sequence)

例：bases = basecount('TAGCTGGCCAAGCGAGCTTG')

答案：bases =

A: 4

C: 5

G: 7

T: 4

2.dimercount(count dimers in a sequence)

例：dimercount('TAGCTGGCCAAGCGAGCTTG')

答案： ans =

AA: 1

AC: 0

AG: 3

AT: 0

CA: 1

CC: 1