I've worked pretty frequently with genome and transcriptome data for several years now, but I'm still not 100% sure I understand the proper usage for certain terminology related to transcripts and transcriptomics. Let me give it my best shot.
- cDNA: in general, this term corresponds to any DNA that is derived from an RNA template via reverse transcription (complementary DNA); however, it is often used to refer to full length cDNAs, DNA sequences that correspond to complete mRNA molecules
- EST: expressed sequence tags correspond to cDNA (sub)sequences obtained from a single read of a cDNA sequencing experiment
- RNA-seq: this refers to the use of high-throughput sequencing technologies to characterize entire transcriptomes, such as by transcript assembly or expression analysis
Here's my concern: I've seen ESTs described as "one-shot" or "single-pass" sequences, which I interpret to mean a single sequence read. However, they are also typically described as being hundreds of base pairs in length (Wikipedia claims about 500-800bp in length max), which (currently) limits this definition to reads derived from Sanger-style sequencing.
Does this mean that a short read derived from a high-throughput sequencing platform is not an EST? Is this distinction based on read length? platform? throughput?
Due to technical limitations, short reads are often assembled before they are used for other downstream analysis. I have sometimes heard the contigs belonging to these assemblies as ESTs, but this doesn't seem to be consistent with the previous definitions.
Is our terminology becoming inconsistent due to the rapid improvements in sequencing technology, or am I missing or misinterpreting something?