ORF predicted from RNA sequence might not be the real Recommend using BED file as input because the longest When FASTA file is provided, searchingįor the longet ORF. The positions of ‘start codon, and ‘stop codon’, When BED file is provided, use the ORF defined in theīED file (the 7th and 8th columns in BED file define The input FASTA or BED fileĬould be a regular text file or compressed file ( *.gz, Genomic sequnences of protein-coding RNAs in FASTA
#IRVUE COMMAND LINE DOWNLOAD#
Note: Users can download prebuilt logit models (Human, Mouse, Fly, Zebrafish) from here Options: -version
Logical to determine if detailed running informationīuild logistic regression model (“”) required by CPAT. Selection according to the “coding probability”.
default=”CPAT_run_info.log”Ĭriteria to select the best ORF: “l”=length, selectionĪccording to the “ORF length” “p”=probability, Line width of output ORFs in FASTA format. Not need to calculate “Fickett score”, “Hexamer score”Īnd “coding probability” for all of them. Possible ORFs, in most cases, the real ORF is ranked Multiple stop codons shouldīe separated by ‘,’.
#IRVUE COMMAND LINE CODE#
Sense strand (or coding strand) is DNA strand thatĬarries the translatable code in the 5′ to 3′ĭirection. Option if FASTA file was provided to ‘-g/–gene’.Īlso search for ORFs from the anti-sense strand. *.fai file along with the original *.fa file within Genome file will be indexed automatically (produce Reference genome sequences in FASTA format. ‘make_hexamer_tab.py’ to make this table out of your ‘make_logitModel.py’ to build logistic regression Human, Mouse, Fly, Zebrafish are availablel. Or compressed file ( *.gz, *.bz2) or accessible URL Input FASTA or BED file could be a regular text file Reference genome (‘-r/–ref’) should be specified. Sequence identifiers (such as Ensembl transcript id) It is recommended to use short and unique The best ORF will be selected (controlled by -best-orf) either by ORF length or coding probability.Ĭommand line options ¶ Options: -versionįormat.In addition to basic ORF information (“ORF frame”, “ORF strand”, “ORF start”, “ORF end”, “ORF sequence”), it also reports “coding probability” for each ORF.The number of ORF reported is controlled by -min-orf and -top-orf. It gives exactly the same results as NCBI ORFfinder does. If model is provided, CPAT can be used as an ORFfinder.Version 3.0.0 is released to address this problem. The 2nd longest ORF of NM_198086 is the real ORF, and the 3rd longest ORF of NM_030915 is the Minor bug fixed regarding the output format.įor many transcripts, the longest ORF may not be the real ORF.
#IRVUE COMMAND LINE UPDATE#
Update “make_logitModel.py” to make it compatible with “cpat.py”. Update “cpat.py” to handle alternative start codens.
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