DNA sequence open reading frames (ORFs) | DNA序列的开放阅读框ORF预测

常见的ORF预测工具

Open Reading Frame Finder - NCBI

ORF Finder - SMS

OrfPredictor  - YSU

基本概念

开放阅读框（英语：Open reading frame；缩写：ORF；其他译名：开放阅读框架、开放读架等）是指在给定的阅读框架中，不包含终止密码子的一串序列。这段序列是生物个体的基因组中，可能作为蛋白质编码序列的部分。基因中的ORF包含并位于开始编码与终止编码之间。由于一段DNA或RNA序列有多种不同读取方式，因此可能同时存在许多不同的开放阅读框架。有一些计算机程序可分析出最可能是蛋白质编码的序列。

关键词：

1. 不包含终止密码子的一串序列；

2. 可能作为蛋白质编码序列的部分；

3. 有多种不同读取方式，因此可能同时存在许多不同的开放阅读框架；

4. 有些工具会用blast比对来提高可信度

 

示例

一段5'-UCUAAAGGUCCA-3'序列。此序列共有3种读取法：

1. UCU AAA GGU CCA
2. CUA AAG GUC
3. UAA AGG UCC

由于UAA为终止编码，因此第三种读取法不具编译出蛋白质的潜力，故只有前两者为开放阅读框架

 

个人当然是推荐使用NCBI大佬开发的工具的啦，发文章可信度高些。

以下是Linux版该工具的说明：

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USAGE   ORFfinder [-h] [-help] [-xmlhelp] [-in Input_File] [-id Accession_GI]     [-b begin] [-e end] [-c circular] [-g Genetic_code] [-s Start_codon]     [-ml minimal_length] [-n nested_ORFs] [-strand Strand] [-out Output_File]     [-outfmt output_format] [-logfile File_Name] [-conffile File_Name]     [-version] [-version-full] [-dryrun]   DESCRIPTION    Searching open reading frames in a sequence   OPTIONAL ARGUMENTS  -h    Print USAGE and DESCRIPTION;  ignore all other parameters  -help    Print USAGE, DESCRIPTION and ARGUMENTS; ignore all other parameters  -xmlhelp    Print USAGE, DESCRIPTION and ARGUMENTS in XML format; ignore all other    parameters  -logfile <File_Out>    File to which the program log should be redirected  -conffile <File_In>    Program's configuration (registry) data file  -version    Print version number;  ignore other arguments  -version-full    Print extended version data;  ignore other arguments  -dryrun    Dry run the application: do nothing, only test all preconditions    *** Input query options (one of them has to be provided):  -in <File_In>    name of file with the nucleotide sequence in FASTA format    (more than one sequence is allowed)    Default = `'  -id <String>    Accession or gi number of the nucleotide sequence    (ignored, if the file name is provided)    Default = `'    *** Query sequence details:  -b <Integer>    Start address of sequence fragment to be processed    Default = `1'  -e <Integer>    Stop address of sequence fragment to be processed (0 - to the end of the    sequence)    Default = `0'  -c <Boolean>    Is the sequence circular? (t/f) *** Under development    Default = `false'    *** Search parameters:  -g <Integer>    Genetic code to use (1-31)    see https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi for details    Default = `1'  -s <Integer>    ORF start codon to use:        0 = "ATG" only        1 = "ATG" and alternative initiation codons        2 = any sense codon    Default = `1'  -ml <Integer>    Minimal length of the ORF (nt)    Value less than 30 is automatically changed by 30.    Default = `75'  -n <Boolean>    Ignore nested ORFs (completely placed within another)    Default = `false'  -strand <String>    Output ORFs on specified strand only (both|plus|minus)    Default = `both'    *** Output options:  -out <File_Out>    Output file name  -outfmt <Integer>    Output options:        0 = list of ORFs in FASTA format        1 = CDS in FASTA format        2 = Text ASN.1        3 = Feature table    Default = `0'

　　

 

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1	ORFfinder -in in.fasta -s 2 -ml 100 -out test.out -outfmt 3