How to create an EST database?

Question

[emmy]

How do you create an EST database? What does EST database contribute to modern day genomics? For a newly discovered organism with unknown genome sequence, how would an EST database for the organism help?

I was wondering if anyone would be able to help answer this question?

[Pierre Lindenbaum]

How do you create an EST database?

echo "create table ESTDB(name TEXT, sequence TEXT);" | sqlite3 est.sqlite3

of course, that's not what you want.

You need to explain what's the goal of your database.

Answer 1

[GenoMax]

While the database bit of this question will become related to bioinformatics (and this forum later on) the EST part is what I will try to tackle now.

Organisms that have "black box" (relatively) genomes EST's are perhaps the low hanging fruit that you can get started on to get an idea of what is "happening" in the genome. It gives you access to information about parts of the genome that are being actively transcribed/translated and can in turn be used to identify those genes/close relatives. This may be very important for genomes that are known to be repetitive/complex/multi-ploidy.

Assuming you are going to use the cheaper Illumina like sequencing methods you can take a stab at assembling the reads into longer transcripts. If you have the budget/expertise to do something like Iso-Seq (PacBio) then you can start getting information about full length EST's as well.