Program in Bioinformatics & Proteomics/Genomics

BPG Databases

 

Dr. Alexei Fedorov's lab can be seen here:  http://bpg.utoledo.edu/~afedorov/lab/


The Exon-Intron Database

Shepelev V., Fedorov A. Advances in the Exon-Intron Database. Briefings in Bioinformatics 2006, 7: 178-185. 

 

New Releases

Species Name EID    
Human, build 37.1 hs37p1.EID.tar.gz    
Mouse, build 37.1 mm37p1.EID.tar.gz    
Cow, build 3.1 Bt3p1.EID.tar.gz  
Human, build 36.1 hs36p1.EID.tar.gz     
Mouse, build 36.1 mm36p1.EID.tar.gz    
Rat, build 4 rn4p1.EID.tar.gz    
Sea Urchin Spur2p1.EID.tar.gz    

 

Release of Exon-Intron Database, September 2005
Species name EID                               

UID

ILD
Human (GenBank 35.1) hs35p1.EID.tar.gz

hs35p1.UID.tar.gz  

hs35p1.ILD.tar.gz  
Mouse (GenBank 34.1) mm34p1.EID.tar.gz  mm34p1.UID.tar.gz   mm34p1.ILD.tar.gz  
Rat (GenBank 3.1) rn3p1.EID.tar.gz   rn3p1.UID.tar.gz   rn3p1.ILD.tar.gz   
Dog (GenBank 2.1) cfa2p1.EID.tar.gz   cfa2p1.UID.tar.gz   cfa2p1.ILD.tar.gz  
Chicken (GenBank 1.1) gga1p1.EID.tar.gz   gga1p1.UID.tar.gz   gga1p1.ILD.tar.gz  
Danio rerio (release Zv4) drzv4.EID.tar.gz   drzv4.UID.tar.gz   drzv4.ILD.tar.gz  
C. elegans (GenBank 2003) ce2003.EID.tar.gz   ce2003.UID.tar.gz   ce2003.ILD.tar.gz  
D. melanogaster (4.1) dm4p1.EID.tar.gz   dm4p1.UID.tar.gz   dm4p1.ILD.tar.gz  
A. thaliana (2004) at2004.EID.tar.gz   at2004.UID.tar.gz   at2004.ILD.tar.gz  
gb149 (original EID) gb149.EID.tar.gz
MOID release 2

September 2005

(MOID_Sept05.tar.gz)    

Instructions README_Sept05  

 

 

 

 

 

 

 

 

 

MOID 3.0 (July 2010,

DOMINO5

http://bpg.utoledo.edu/~aprakash/orthologous_introns.html

Please cite the reference at the top of this page (Shepelev and Fedorov) when using the Exon-Intron Database in your research.
 

README  - Explanations about new releases of Exon-Intron Database (EID)

SNO.pl   - This program searches for conserved structures characteristic for C/D box snoRNA

TARGETmrna.pl   - This program searches for the targets of snoRNA antisense elements among all mRNA sequences of human, mouse and rat

siRNA.pl - This program scans the entire set of human introns searching for stem-loop hairpin structures with perfect stems spanning at least 21 nucleotides and with short 0 to 80 nucleotides loops.

snoRNA.r3.pl - The latest version of snoRNA.pl

57snoRNA   

FR3D Page

    

Questions or Comments:

Alexei Fedorov, Ph.D.
Associate Professor, Department of Medicine
Head of Bioinformatics Lab
University of Toledo Health Science Campus
3125 Transverse Dr.
Toledo, OH 43614

Link to Alexei Fedorov home page

Phone: (419)-383-5270
Fax: (419)-383-3102
E -mail: alexei.fedorov@utoledo.edu

Last Updated: 3/22/15