#!/bin/bash # This shell script folds an RNA or DNA sequence and creates output # files. export _POSIX2_Version=0 export Package_URL="http://mfold.rna."
$mfold Usage is mfold SEQ='file_name' with optional parameters: [ AUX='auxfile_name' ] [ RUN_TYPE=text (default) or html ] [ NA=RNA (default) or DNA ] [ LC=sequence type (default = linear) ] [ T=temperature (default = 37 deg C) ] [ P=percent (default = 5) ] [ NA_CONC=Na+ molar concentration (default = 1.0) ] [ MG_CONC=Mg++ molar concentration (default = 0.0) ] [ W=window parameter (default - set by sequence length) ] [ MAXBP=max base pair distance (default - no limit) ] [ MAX=maximum number of foldings to be computed (default 100) ] [ MAX_LP=maximum bulge/interior loop size (default 30) ] [ MAX_AS=maximum asymmetry of a bulge/interior loop (default 30) ] [ ANN=structure annotation type: none (default), p-num or ss-count ] [ MODE=structure display mode: auto (default), bases or lines ] [ LAB_FR=base numbering frequency ] [ ROT_ANG=structure rotation angle ] [ START=5' base # (default = 1)] [ STOP=3' base # (default = end) ] [ REUSE=NO/YES (default=NO) reuse existing .sav file ]
对于软件安装包里面自带的测试序列,我们可以这样运行:
$mfold SEQ='test.txt' # 不知道为什么我的报错了,如下: mfold version 3.6 REUSE= NO test.txt.pnt created. Sequence length is 221 Folding at 37 degrees using version 3.0 dat files. Save file created using nafold. Save file is empty. No foldings. Job Aborted
542K Mar 21 2009 mdv1.37.ct 5.1K Mar 21 2009 mdv1.37.ext 13K Mar 21 2009 mdv1.37.plot 39 Mar 21 2009 mdv1.dG 61K Oct 24 2009 mdv1.jpg 239 Nov 19 2009 mdv1-local.seq 33 Nov 19 2009 mdv1.log 51K Oct 24 2009 mdv1.pdf 14K Mar 21 2009 mdv1.plot 12K Oct 24 2009 mdv1.png 21K Oct 24 2009 mdv1.ps 109 Mar 21 2009 mdv1.run 4.0K Jan 11 16:12 mfold
相当于你在网页工具里面提交序列,选择参数,然后运行拿到的交互式结果。
其它编程语言的mfold
比如:https:///project/seqfold/, seqfold is an implementation of the Zuker, 1981 dynamic programming algorithm, the basis for UNAFold/mfold, with energy functions from SantaLucia, 2004 (DNA) and Turner, 2009 (RNA).