FASTA应用.doc

FASTA应用专题实践摘 要 本文使用perl语言编写程序实现了对序列的分离和由单字母到三字母的转化。关键词：perl 分离 序列ABSTRACT This article uses the perl programming language to achieve a separation of the sequence and by the single-letter to three-letter conversion.Key words：perl separation sequence一 文本序列所要分离和转化的序列为：1A23:A|PDBID|CHAIN|SEQUENCEAQYEDGKQYTTLEKPVAGAPQVLEFFSFFCPHCYQFEEVLHISDNVKKKLPEGVKMTKYHVNFMGGDLGKDLTQAWAVAMALGVEDKVTVPLFEGVQKTQTIRSASDIRDVFINAGIKGEEYDAAWNSFVVKSLVAQQEKAAADVQLRGVPAMFVNGKYQLNPQGMDTSNMDVFVQQYADTVKYLSEKK1AAR:B|PDBID|CHAIN|SEQUENCEMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG1AG2:A|PDBID|CHAIN|SEQUENCEGLGGYMLGSAMSRPMIHFGNDWEDRYYRENMYRYPNQVYYRPVDQYSNQNNFVHDCVNITIKQHTVTTTTKGENFTETDVKMMERVVEQMCVTQYQKESQAYY1AJ3:A|PDBID|CHAIN|SEQUENCEAKLNESHRLHQFFRDMDDEESWIKEKKLLVSSEDYGRDLTGVQNLRKKHKRLEAELAAHEPAIQGVLDTGKKLSDDNTIGKEEIQQRLAQFVDHWKELKQLAAARGQRLE1ARR:B|PDBID|CHAIN|SEQUENCEMKGMSKMPQFNLRWPREVLDLVRKVAEENGRSVNSEIYQRVMESFKKEGRIGA1BPI:A|PDBID|CHAIN|SEQUENCERPDFCLEPPYTGPCKARIIRYFYNAKAGLCQTFVYGGCRAKRNNFKSAEDCMRTCGGA1BNI:C|PDBID|CHAIN|SEQUENCE二 程序及注释2.1程序 所编写的perl程序为：其中有关单字母到三字母的转化引自生物化学课本。#!/usr/bin/perl open(INFILE, F:学习论文生信文本.txt) or die “Cant open data.txt: $!”; $i=0;while() if($_=/) #以为开头分离序列 $i=$i+1; print”第$i个序列为：n”; if( $_ = /A-Z/ ) $_=s/G/Gly /g; $_=s/A/Ala /g; $_=s/V/Val /g; $_=s/L/Leu /g; $_=s/I/Ile /g; $_=s/F/Phe /g; # $_=s/P/Pro /g; #单字母到三字母的转化 $_=s/W/Trp /g; # $_=s/S/Ser /g; # $_=s/Y/Tyr /g; $_=s/C/Cys /g; $_=s/M/Met /g; $_=s/N/Asn /g; $_=s/Q/Gln /g; $_=s/T/Thr /g; $_=s/D/Asp /g; $_=s/E/Glu /g; $_=s/K/Lys /g; $_=s/R/Arg /g; $_=s/H/His /g; print”$_”; close (INFILE);2.2结果运行结果为：第1个序列为：Ala Gln Thr yr Glu Asp Gly Lys Gln Thr yr Thr Thr Leu Glu Lys Pro Val Ala Gly Ala Pro Gln Val Leu Glu Pro he Pro he Ser Pro he Pro he Cys Pro His Cys Thr yr Gln Pro he Glu Glu Val Leu His Ile Ser Asp Asn Val Lys Lys Lys Leu Pro Glu Gly Val Lys Met Thr Lys Thr yr His Val Asn Pro he Met Gly Gly Asp Leu Gly Lys Asp Leu Thr Gln Ala Thr rp Ala Val Ala Met Ala Leu Gly Val Glu Asp Lys Val Thr Val Pro Leu Pro he Glu Gly Val Gln Lys Thr Gln Thr Ile Arg Ser Ala Ser Asp Ile Arg Asp Val Pro he Ile Asn Ala Gly Ile Lys Gly Glu Glu Thr yr Asp Ala Ala Thr rp Asn Ser Pro he Val Val Lys Ser Leu Val Ala Gln Gln Glu Lys Ala Ala Ala Asp Val Gln Leu Arg Gly Val Pro Ala Met Pro he Val Asn Gly Lys Thr yr Gln Leu Asn Pro Gln Gly Met Asp Thr Ser Asn Met Asp Val Pro he Val Gln Gln Thr yr Ala Asp Thr Val Lys Thr yr Leu Ser Glu Lys Lys 第2个序列为：Met Gln Ile Pro he Val Lys Thr Leu Thr Gly Lys Thr Ile Thr Leu Glu Val Glu Pro Ser Asp Thr Ile Glu Asn Val Lys Ala Lys Ile Gln Asp Lys Glu Gly Ile Pro Pro Asp Gln Gln Arg Leu Ile Pro he Ala Gly Lys Gln Leu Glu Asp Gly Arg Thr Leu Ser Asp Thr yr Asn Ile Gln Lys Glu Ser Thr Leu His Leu Val Leu Arg Leu Arg Gly Gly 第3个序列为：Gly Leu Gly Gly Thr yr Met Leu Gly Ser Ala Met Ser Arg Pro Met Ile His Pro he Gly Asn Asp Thr rp Glu Asp Arg Thr yr Thr yr Arg Glu Asn Met Thr yr Arg Thr yr Pro Asn Gln Val Thr yr Thr yr Arg Pro Val Asp Gln Thr yr Ser Asn Gln Asn Asn Pro he Val His Asp Cys Val Asn Ile Thr Ile Lys Gln His Thr Val Thr Thr Thr Thr Lys Gly Glu Asn Pro he Thr Glu Thr Asp Val Lys Met Met Glu Arg Val Val Glu Gln Met Cys Val Thr Gln Thr yr Gln Lys Glu Ser Gln Ala Thr yr Thr yr 第4个序列为：Ala Lys Leu Asn Glu Ser His Arg Leu His Gln Pro he Pro he Arg Asp Met Asp Asp Glu Glu Ser Thr rp Ile Lys Glu Lys Lys Leu Leu Val Ser Ser Glu Asp Thr yr Gly Arg Asp Leu Thr Gly Val Gln Asn Leu Arg Lys Lys His Lys Arg Leu Glu Ala Glu Leu Ala Ala His Glu Pro Ala Ile Gln Gly Val Leu Asp Thr Gly Lys Lys Leu Ser Asp Asp Asn Thr Ile Gly Lys Glu Glu Ile Gln Gln Arg Leu Ala Gln Pro he Val Asp His Thr rp Lys Glu Leu Lys Gln Leu Ala Ala Ala Arg Gly Gln Arg Leu Glu 第5个序列为：Met Lys Gly Met Ser Lys Met Pro Gln Pro he Asn Leu Arg Thr rp Pro Arg Glu Val Leu Asp Leu Val Arg Lys Val Ala Glu Glu Asn Gly Arg Ser Val Asn Ser Glu Ile Thr yr Gln Arg Val Met Glu Ser Pro he Lys Lys Glu Gly Arg Ile Gly Ala 第6个序列为：Arg Pro Asp Pro he Cys Leu Glu Pro Pro Thr yr Thr Gly Pro Cys