Restriction Fragment DataBase (RFDB)
Use the query interface of RFDB to investigate in silico the predicted fragments or amplicons that can be detected by RFDD.
Search fragments by transcripts
In this section of the RFDB page, you can search for fragments by definig some criteria.
All transcripts in RFDB come from the RefSeq database (visit here).
You can retrieve a transcript by its RefSeq accession number if you already know it.
Or you can search by entering one or several terms that can be the name or at least one synonym. Do not use too general terms in order to avoid huge and inexploitable query results.
You also have to select the restriction enzyme by which this transcript is digested in silico in RFDB.
Finally you may select or not a species name. "All" will result in a list of transcripts from all organisms proposed by our website.
In a second step, a link on each transcript of the list will lead you to the detailed view of restriction fragments (see below).
Search transcripts by fragments
Use this second section to search for transcripts that contain fragments of your interest.
Therefore, you may define :
- the restriction enzyme that could generate the fragment
- the species of interest
- the size of the fragment : it can be a size range or a given size (same value in both size inputs)
- optionnaly you can restrict to a selective trinucleotide : the 3 trinucleotides on one (or maybe both) of the two 5' possible ends of the fragment.
Transcript list
The two types of query lead you to a list of transcripts.
No result means that no transcript seems to correspond to your criteria (name, ID, fragment ...) or this transcript doesn't contain at least two restriction sites.
The first column gives a number (arbitray rank) of the transcript in the list.
The second one is the RefSeq number (it links to a RefSeq file on the PBIL server). Besides is the full RefSeq definition.
The last column is the number of fragments generated in silico. Click on the number to get a detailed view of the fragments.
Detailed view of restriction fragments
This page presents all the restriction fragments of a given transcript (double stranded cDNA).
Each line defines a fragment.
The first column is the rank of the fragment.
The second one, its size in bases before ligation of the adapters (selective and fluorescent).
The third, the size of the product of amplification (amplicon size).
The fourth one gives the starting position of the restriction fragment.
The next one gives you a design of the fragment. Blue bases are the remaining of the restriction site. The two possible RFDD selective trinucleotide of the fragment are represented in red.
The last column gives the ending position of the fragment.
You can print this page by simply clicking on the printer icon on top. That will only print the area contained in the blue dashed border.
Any more data?
If you are working on a species that is not present in RFDB, ask us. We can update RFDB and enclose new species, new enzymes and new organisms. Note that as the RefSeq database is evolving, RFDB can follow!
Technical notes
RFDD database is build under PostgreSQL SGBD.
The following picture shows the database scheme :
A back-office on this website allows administrators to easily update the database accordingly to new release of RefSeq.
Last update was on August 27, 2008, 9:42 am . By sending us an email, you can request for a new update.
If you are interested to get the database dump, simply send us an email.
