FASTA程序.docx

FASTA程序

第一篇：FASTA程序FASTA文件>1A23:A|PDBID|CHAIN|SEQUENCEAQYEDGKQYTTLEKPVAGAPQVLEFFSFFCPHCYQFEEVLHISDNVKKKLPEGVKMTKYHVNFMGGDLGKDLTQAWAVAMALGVEDKVTVPLFEGVQKTQTIRSASDIRDVFINAGIKGEEYDAAWNSFVVKSLVAQQEKAAADVQLRGVPAMFVNGKYQLNPQGMDTSNMDVFVQQYADTVKYLSEKK>1AAR:B|PDBID|CHAIN|SEQUENCEMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG>1AG2:A|PDBID|CHAIN|SEQUENCEGLGGYMLGSAMSRPMIHFGNDWEDRYYRENMYRYPNQVYYRPVDQYSNQNNFVHDCVNITIKQHTVTTTTKGENFTETDVKMMERVVEQMCVTQYQKESQAYY>1AJ3:A|PDBID|CHAIN|SEQUENCEAKLNESHRLHQFFRDMDDEESWIKEKKLLVSSEDYGRDLTGVQNLRKKHKRLEAELAAHEPAIQGVLDTGKKLSDDNTIGKEEIQQRLAQFVDHWKELKQLAAARGQRLE>1ARR:B|PDBID|CHAIN|SEQUENCEMKGMSKMPQFNLRWPREVLDLVRKVAEENGRSVNSEIYQRVMESFKKEGRIGA程序代码：#!/usr/bin/perl#Perl程序的标志。open(INFILE,'H:bioFastA.txt')ordiedie“Can'topendata.txt:$!”;#打开文件以进行修改操作！这一行放置待提序列文件的路径while()#将读入的_整行_内容赋值给$_.{if($_=~/^>/)#如果某行开头是“>”，则进行下面的操作,在行首加上注释。{print“reference:”;print$_,“n”;}else{$_=~s/A/Ala./g;#把氨基酸单字母改成三字母。用到替换的正则表达式。$_=~s/G/Gly./g;$_=~s/S/Ser./g;$_=~s/V/Val./g;$_=~s/I/Ile./g;$_=~s/L/Leu./g;$_=~s/T/Thr./g;$_=~s/Y/Tyr./g;$_=~s/P/Pro./g;$_=~s/F/Phe./g;$_=~s/H/His./g;$_=~s/D/Asp./g;$_=~s/M/Met./g;$_=~s/E/Glu./g;$_=~s/R/Arg./g;$_=~s/W/Trp./g;$_=~s/Q/Gln./g;$_=~s/K/Lys./g;$_=~s/C/Cys./g;$_=~s/N/Asn./g;print“sequence:”;print$_,“n”;#如果开头不是“>”，就进行替换并且输出.}}close(INFILE);#关掉文件1、安装Perl.exe和Tool.exe。2、打开Untitledpig.cgi。3、记得改路径，你下载的FastA.Txt放到哪个路径就改成相应的。在Open语句中改。4、点击运行就可以了。结果会显示如下：reference:>1A23:A|PDBID|CHAIN|SEQUENCEsequence:Ala.Gln.Tyr.Glu.Asp.Gly.Lys.Gln.Tyr.Thr.Thr.Leu.Glu.Lys.Pro.Val.Ala.Gly.Ala.Pro.Gln.Val.Leu.Glu.Phe.Phe.Ser.Phe.Phe.Cys.Pro.His.Cys.Tyr.Gln.Phe.Glu.Glu.Val.Leu.His.Ile.Ser.Asp.Asn.Val.Lys.Lys.Lys.Leu.Pro.Glu.Gly.Val.Lys.Met.Thr.Lys.Tyr.His.Val.Asn.Phe.Met.Gly.Gly.Asp.Leu.Gly.Lys.Asp.Leu.Thr.Gln.Ala.Trp.Ala.Val.Ala.Met.sequence:Ala.Leu.Gly.Val.Glu.Asp.Lys.Val.Thr.Val.Pro.Leu.Phe.Glu.Gly.Val.Gln.Lys.Thr.Gln.Thr.Ile.Arg.Ser.Ala.Ser.Asp.Ile.Arg.Asp.Val.Phe.Ile.Asn.Ala.Gly.Ile.Lys.Gly.Glu.Glu.Tyr.Asp.Ala.Ala.Trp.Asn.Ser.Phe.Val.Val.