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|SEQUENCE AQYEDGKQYTTLEKPVAGAPQVLEFFSFFCPHCYQFEEVLHISDNVKKKLPEGVKMTKYHVNFMGGDLGKDLTQAWAVAMALGVEDKVTVPLFEGVQKTQTIRSASDIRDVFINAGIKGEEYDAAWNSFVVKSLVAQQEKAAADVQLRGVPAMFVNGKYQLNPQGMDTSNMDVFVQQYADTVKYLSEKK 1AAR:B|PDBID|CHAIN|SEQUENCE MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG 1AG2:A|PDBID|CHAIN|SEQUENCE GLGGYMLGSAMSRPMIHFGNDWEDRYYRENMYRYPNQVYYRPVDQYSNQNNFVHDCVNITIKQHTVTTTTKGENFTETDV KMMERVVEQMCVTQYQKESQAYY 1AJ3:A|PDBID|CHAIN|SEQUENCE AKLNESHRLHQFFRDMDDEESWIKEKKLLVSSEDYGRDLTGVQNLRKKHKRLEAELAAHEPAIQGVLDTGKKLSDDNTIGKEEIQQRLAQFVDHWKELKQLAAARGQRLE 1ARR:B|PDBID|CHAIN|SEQUENCE MKGMSKMPQFNLRWPREVLDLVRKVAEENGRSVNSEIYQRVMESFKKEGRIGA 1BPI:A|PDBID|CHAIN|SEQUENCE RPDFCLEPPYTGPCKARIIRYFYNAKAGLCQTFVYGGCRAKRNNFKSAEDCMRTCGGA 1BNI: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 “Can’t open data.txt: $!”; $i=0; while(INFILE) { if($_=~//) { $i=$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