Editing Sequence assembly (section)

=== EST ===

[[Expressed Sequence Tag|Expressed sequence tag]] or EST assembly was an early strategy, dating from the mid-1990s to the mid-2000s, to assemble individual genes rather than whole genomes.<ref name="Nagaraj_2007">{{cite journal | vauthors = Nagaraj SH, Gasser RB, Ranganathan S | title = A hitchhiker's guide to expressed sequence tag (EST) analysis | journal = Briefings in Bioinformatics | volume = 8 | issue = 1 | pages = 6–21 | date = January 2007 | pmid = 16772268 | doi = 10.1093/bib/bbl015 }}</ref> The problem differs from genome assembly in several ways. The input sequences for EST assembly are fragments of the transcribed [[Messenger RNA|mRNA]] of a cell and represent only a subset of the whole genome.<ref name="Nagaraj_2007" /> A number of algorithmical problems differ between genome and EST assembly. For instance, genomes often have large amounts of repetitive sequences, concentrated in the intergenic regions. Transcribed genes contain many fewer repeats, making assembly somewhat easier. On the other hand, some genes are expressed (transcribed) in very high numbers (e.g., [[housekeeping gene]]s), which means that unlike whole-genome shotgun sequencing, the reads are not uniformly sampled across the genome.

EST assembly is made much more complicated by features like (cis-) [[alternative splicing]], [[trans-splicing]], [[single-nucleotide polymorphism]], and [[post-transcriptional modification]]. Beginning in 2008 when [[RNA-Seq]] was invented, EST sequencing was replaced by this far more efficient technology, described under [[de novo transcriptome assembly]].