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:
- UCU AAA GGU CCA
- CUA AAG GUC
- 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:
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‘
ORFfinder -in in.fasta -s 2 -ml 100 -out test.out -outfmt 3
原文地址:https://www.cnblogs.com/leezx/p/8645696.html
时间: 2024-10-14 22:50:13