Useful Links of Bioinformatics

Gene Prediction

ORF Finder  www.ncbi.nlm.nih.gov/gorf/gorf.html
SoftBerry Genefinding  www.softberry.com/berry.phtml?topic=index&group=programs&subgroup=gfind
GENESCAN  genes.mit.edu/GENSCAN.html
GRAIL  compbio.ornl.gov/grailexp/
Twinscan  http://genes.cs.wustl.edu/
GeneMark  exon.gatech.edu/genemark/
Amigene  www.genoscope.cns.fr/agc/tools/amigene/Form/form.php


Promoter Site Prediction

Neural Network Promoter
Prediction
 www.fruitfly.org/seq_tools/promoter.html
PROSCAN  www-bimas.cit.nih.gov/molbio/proscan/
CorePromoter  http://rulai.cshl.org/tools/genefinder/CPROMOTER/index.htm
PROMOTER SCAN II  www.molbiol.ox.ac.uk/promoterscan.htm


Pick Primer/Restriction Enzyme Site Map

Primer3  cbr-rbc.nrc-cnrc.gc.ca/cgi-bin/primer3_www.cgi


Topology Prediction of Membrane Proteins

SOSUI  bp.nuap.nagoya-u.ac.jp/sosui/
TMHMM  www.cbs.dtu.dk/services/TMHMM/
DAS  www.sbc.su.se/~miklos/DAS/maindas.html
HMMTOP  www.enzim.hu/hmmtop/
Meta predictprotein  www.predictprotein.org  (등록후 사용가능 : 유료싸이트로 전환되어짐)
Toppred  bioweb.pasteur.fr/seqanal/interfaces/toppred.html
MEMSAT  bioinf.cs.ucl.ac.uk/psipred/
Tmpred  www.ch.embnet.org/software/TMPRED_form.html
PRED-TMR  o2.biol.uoa.gr/PRED-TMR/input.html
TMAP  bioweb.pasteur.fr/seqanal/interfaces/tmap.html


Signal Peptide Prediction

SignalP  www.cbs.dtu.dk/services/SignalP


Protein 3D Structure

PDB  www.rcsb.org


Protein 3D Selection

PDB-REPRDB  mbs.cbrc.jp/pdbreprdb-cgi/reprdb_menu.pl


2D Prediction

PSIPRED  bioinf.cs.ucl.ac.uk/psipred/
PROF  www.aber.ac.uk/~phiwww/prof/
NNPREDICT  www.cmpharm.ucsf.edu/~nomi/nnpredict.html
PSA  bmerc-www.bu.edu/psa/


Homology Modelling : Webserver

3D-JIGSAW  www.bmm.icnet.uk/~3djigsaw/
CPHmodels  www.cbs.dtu.dk/services/CPHmodels/
SWISS-MODEL  www.expasy.ch/swissmod/


3D Profiling

LIBRA libra.ddbj.nig.ac.jp/top-e.html
3D-PSSM  www.sbg.bio.ic.ac.uk/~3dpssm/
FUGUE  www-cryst.bioc.cam.ac.uk/~fugue/
123D  www.softberry.com/berry.phtml


Annotation 3D Structure Visualization Annotation

RasMol  www.umass.edu/microbio/rasmol/
Chime  www.umass.edu/microbio/rasmol/
Protein Explorer  www.umass.edu/microbio/chime/explorer
Cn3D  www.ncbi.nlm.nih.gov/Structure/CN3D/cn3d.shtml
MPEx  blanco.biomol.uci.edu/mpex/
MOLMOL  www.mol.biol.ethz.ch/wuthrich/software/molmol/
Moiscript  www.avatar.se/molscript/
Raster3D  www.bmsc.washington.edu/raster3d/raster3d.html
GRASP  trantor.bioc.columbia.edu/grasp/
GRASS  honiglab.cpmc.columbia.edu/cgi-bin/GRASS/surfserv_enter.cgi
JOY  www-cryst.bioc.cam.ac.uk/cgi-bin/joy.cgi
TOPS  www.sander.embl-ebi.ac.uk/tops/
LIGPLOT  www.biochem.ucl.ac.uk/bsm/ligplot/ligplot.html


RNA 2D Prediction

Mfold  bioweb.pasteur.fr/seqanal/interfaces/mfold-simple.html
Vienna RNA Package  www.tbi.univie.ac.at/~ivo/RNA/ (다운로드후 설치하여 사용)
RNa secondary structure
prediction
 www.genebee.msu.su/services/rna2_reduced.html (시각적인 데이터 전송)


Pathway

KEGG PATHWAY  www.genome.ad.jp/kegg/


2D Electrophoresis Analysis

SEISS-2DPAGE  www.expasy.ch/ch2d/ch2d-top.html
WORLD-2DPAGE  www.expasy.ch/ch2d/2d-index.html
YPM  www.ibgc.u-bordeaux2.fr/YPM/
Cyano2Dbase  www.kazusa.or.jp/cyano/Synechocystis/cyano2D/
2-D PAGE Database  proteomics.cancer.dk/


Expression Profile

KEGG EXPRESSION  www.genome.ad.jp/dbget-bin/get_htext?Exp_DB+-n+B
Axeldb  www.dkfz-heidelberg.de/abt0135/axeldb.htm
MAGEST  www.genome.ad.jp/magest/
Stanford Microarray Database  genome-www5.stanford.edu/MicroArray/SMD/