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几种常见的序列蛋白编码能力预测工具 | ncRNAs | lncRNA

时间:2018-03-18 10:27:17      阅读:2369      评论:0      收藏:0      [点我收藏+]

标签:FQ   ack   tin   frame   预测   tis   elm   oba   die   

CPC(http://cpc.cbi.pku.edu.cn/)

可在线使用
a Support Vector Machine-based classifier, named Coding Potential Calculator (CPC), to assess the protein-coding potential of a transcript based on six biologically meaningful sequence features.
Coding Potential Calculator distinguish protein-coding from non-coding RNAs based on the sequence features of the input transcripts. Our preliminary performance assessment suggests the CPC can reliably discriminate the coding and non-coding transcripts in ~98% accuracy. We provide an online version of CPC here.
自称有98%的准确率

bin/run_predict.sh (input_seq) (result_in_table) (working_dir) (result_evidence)

CPC RESULTS (The first column is input sequence ID; the second column is input sequence length; the third column is coding status and the four column is the coding potential score (the "distance" to the SVM classification hyper-plane in the features space).)

AF282387	528	coding	3.32462
Tsix_mus	4300	noncoding	-1.30047

HOMO EVIDENCE
ORF EVIDENCE

AF282387	ORF_FRAMEFINDER	4	529	99.43	109.41	Full
Tsix_mus	ORF_FRAMEFINDER	4077	4206	3.00	27.50	Full

FRAME FINDER

>AF282387 Filobasidiella neoformans calcineurin B regulatory subunit (CNB1) mRNA, complete cds [framefinder (3,528) score=109.41 used=99.43% {forward,strict} ]
MGAAESSMFNSLEKNSNFSGPELMRLKKRFMKLDKDGSGSIDKDEFLQIPQIANNPLAHR
MIAIFDEDGSGTVDFQEFVGGLSAFSSKGGRDEKLRFAFKVYDMDRDGYISNGELYLVLK
QMVGNNLKDQQLQQIVDKTIMEADKDGDGKLSFEEFTQMVASTDIVKQMTLEDLF
>Tsix_mus NR_002844.1 Mus musculus X (inactive)-specific transcript, antisense (Tsix) on chromosome X [framefinder (4076,4205) score=27.50 used=3.00% {forward,strict} ]
MKGYVLKLSSWAGEIAQWLGVLTALPEGLSSILNNFVVAHSHL

BLAST RESULT

PLEK

an efficient alignment-free computational tool to distinguish lncRNAs from mRNAs in RNA-seq transcriptomes of species lacking reference genomes.

 

几种常见的序列蛋白编码能力预测工具 | ncRNAs | lncRNA

标签:FQ   ack   tin   frame   预测   tis   elm   oba   die   

原文地址:https://www.cnblogs.com/leezx/p/8594138.html

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