幾種常見的序列蛋白編碼能力預測工具 | ncRNAs | lncRNA
CPC（http://cpc.cbi.pku.edu.cn/）
可在線使用
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.
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} ]
MKGYVLKLSSWAGEIAQWLGVLTALPEGLSSILNNFVVAHSHLBLAST RESULT
PLEK
an efficient alignment-free computational tool to distinguish lncRNAs from mRNAs in RNA-seq transcriptomes of species lacking reference genomes.
幾種常見的序列蛋白編碼能力預測工具 | ncRNAs | lncRNA