I'm interested primarily on use of ESTs on de novo methods for gene finding, another question is: what are the differences between de novo and ab initio methods?
ESTs = Expressed Sequence Tags , they date back from when we were doing Sanger sequencing on cloned cDNAs . I would assume this term is not used anymore for 'transcript sequencing' nowadays. They are (were) used in gene prediction as prove of expression of a given region in the genome, hence point to gene locations.
Not sure what you mean with difference between de-novo and ab-initio. Ab-initio usually points to gene prediction approaches that do not use any external evidence (such as ESTs, transcripts, proteins, ... ) they work solely based on properties that can be derived from the genomic sequence itself. The counterpart is called similarity or homology based prediction: those methods use protein, EST, ... information to locate potential gene locations in the genome. With 'de-novo' you perhaps mean that NGS reads are first being (de-novo) assembled into transcripts before they are used in gene prediction (=beneficial because they more resemble complete genes/transcripts)
i'm refering to https://academic.oup.com/bioinformatics/article/24/5/637/202844
ah, in this case they mean with de-novo :the process of finding genes in a new genomic sequence. de-novo as in find genes in a genome, not mapping known genes to the genome. I always felt it's a bit of an unfortunate naming but it points to the whole gene prediction process rather then to a specific approach (such as those I mentioned in my answer)
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