Question

difference between alignment based and de novo approaches to protein coding sequnce prediction(gene prediction)

Answer 1

Gene prediction:
It is a method to determine the position of a particular coding gene in the given complete genomic sequence of any organism. Functional protein sequenced will start with a start codon and end with a stop codon.

De novo approach for gene prediction:
It involves statistical models to predict gene structure by using one or more genomes as their input sequences. It doesnt need any cDNA sequence or other expressional data for gene prediction. Even if cDNA sequences are available this technique ignores them and predicts completely novel genes. In result they are less accurate than expression based methods of gene prediction which use full length cDNA sequences.

Sequence alignment for gene prediction:
Sequence alignment is a technique in which sequences of DNA, RNA or protein are used to identify the regions of similar structure, function and evolutionary relationship. In de novo there is no use of reference sequence for alignment while here another sequence is used for reference which provides more accurate result compare to de novo sequencing. Its accuracy is comparatively higher than de novo because of evolutionary related genome sequences which reliably increases sensitivity and specificity of gene prediction.


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