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  • Matlab Multialign

Matlab Multialign

Gönderim Mayıs 21st, 2014

Biyoinformatik alaninda multi alignment islevini gerceklestirmeye yarayan multialign komutunun nasil kullanilacagi hakkinda bilgiyi makale icerisinden edinebilirsiniz. Ayni zamanda uygulamayi yaparken ilgili fasta file’larin icerikleride bulunmaktadir.

 

Fasta File

>gi|455997|gb|AAA16334.1| beta-globin [Homo sapiens]
MVHLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPKVKAHGKKVLG
AFSDGLAHLDNLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVAN
ALAHKYH

>gi|44955888|ref|NP_976312.1| myoglobin [Homo sapiens]
MGLSDGEWQLVLNVWGKVEADIPGHGQEVLIRLFKGHPETLEKFDKFKHLKSEDEMKASEDLKKHGATVL
TALGGILKKKGHHEAEIKPLAQSHATKHKIPVKYLEFISECIIQVLQSKHPGDFGADAQGAMNKALELFR
KDMASNYKELGFQG

>gi|10864065|ref|NP_067080.1| neuroglobin [Homo sapiens]
MERPEPELIRQSWRAVSRSPLEHGTVLFARLFALEPDLLPLFQYNCRQFSSPEDCLSSPEFLDHIRKVML
VIDAAVTNVEDLSSLEEYLASLGRKHRAVGVKLSSFSTVGESLLYMLEKCLGPAFTPATRAAWSQLYGAV
VQAMSRGWDGE

>gi|313507159|pdb|1CCR|A Chain A, Structure Of Rice Ferricytochrome C At 2.0 Angstroms Resolution
XASFSEAPPGNPKAGEKIFKTKCAQCHTVDKGAGHKQGPNLNGLFGRQSGTTPGYSYSTADKNMAVIWEE
NTLYDYLLNPXKYIPGTKMVFPGLXKPQERADLISYLKEATS

>gi|157830108|pdb|1AVU|A Chain A, Trypsin Inhibitor From Soybean (Sti)
DFVLDNEGNPLENGGTYYILSDITAFGGIRAAPTGNERCPLTVVQSRNELDKGIGTIISSPYRIRFIAEG
HPLSLKFDSFAVIMLCVGIPTEWSVVEDLPEGPAVKIGENKDAMDGWFRLERVSDDEFNNYKLVFCPQQA
EDDKCGDIGISIDHDDGTRRLVVSKNKPLVVQFQKLDKESL

Matlab Kodu :

clear all;
close all;
clc;

% http://www.ncbi.nlm.nih.gov
seqBetaGlo = fastaread(‘betaGlobin.fasta’);
seqMyoGlo = fastaread(‘myoGlobin.fasta’);
seqNeuGlo = fastaread(‘neuroGlobin.fasta’);
seqSoyBean = fastaread(‘soybean.fasta’);
seqRice = fastaread(‘rice.fasta’);

seqBG = seqBetaGlo.Sequence;
seqMG = seqMyoGlo.Sequence;
seqNG = seqNeuGlo.Sequence;
seqSB = seqSoyBean.Sequence;
seqR = seqRice.Sequence;

seqs = {seqBG,seqMG,seqNG,seqSB,seqR};
multialign(seqs)

Ekran Ciktisi

MVHLTPE————————EKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPKVKAHGKKVLGAFSDG

LAHLDNLKGTFATLSEL—HCDKLHVDPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVANAL

AHKY——-HMGLSDGE———————–WQLVLNVWGKVEADIPGHGQEVLIRLFKGHPETLEKFDKFKHLKSEDEMKASEDLKKHGATVLTALGG

ILKKKGHHEAEIKPLAQS—HATKHKIPVKYLEFISECIIQVLQSKHPGDFGADAQGAMNKALELFRKDM

ASNYKELGFQ-GMERPEPE————————LIRQSWRAVSRSPLEHGTVLFARLFALEPDLLPLFQYNCRQFSSPEDCLSSPEFLDHIRKVMLVIDAAVTN

VEDLSSLEEYLASL-GRKHRAVGVKLSSFSTVGESLLYMLEKCLGPAFTPATRAAWSQLYGAVVQAMSRG

WDG—–E
DFVLDNEGNPLENGGTYYILSDITAFGGIRAAPTGNERCPLTVVQSRNELDKGIGTIISSPYRIRFIAEGHPL

SLKFDSFAVIMLCVGIPTEWSVVEDLPEGPAVKIGENKDAMDGWFRLERVSDDEFNNYKLVFCPQQAED

DKCGDIGISIDHDDGTRRLVVSKNKPLVVQFQKLDKESL
XASFSE———————APPGNPKAGEKIFKTKCAQCHTVDKGAGHKQGPNLNGLFGRQSG–TTPGYSYSTADKNMAVIWEENTLYDYLLNPXKYIPGTKMVFPGLXKPQERAD——————————

—————-LISYLKEATS

Keyifli Calismalar Dilerim.

Etiketler: , , ,
Bulundugu Konu Etiketleri Akademik, BioInformatic, Matlab, Yazilim |

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