Useful Links of Bioinformatics
Pulic Web Site
GenBank www.ncbi.nlm.nih.gov/Genbank/index.html
EMBL www.ebi.ac.uk/embl/index.html
DDBJ www.ddbj.nig.ac.jp/index-j.html

Human Genome Sequence / Gene Information
UCSC genome browser genome.ucsc.edu/
GeneCards www.genecards.org
OMIM www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=OMIM

Microbial Genome / Gene Information
TIGR Database www.tigr.org/

Codon usage
Codon Usage Database www.kazusa.or.jp/codon

Motif Search
InterPro www.ebi.ac.uk/interpro/
InterProscan www.ebi.ac.uk/InterProScan
MOTIF motif.genome.ad.jp/

Multiple Alignment
ClustalW clustalw.genome.ad.jp/
www.ebi.ac.uk/clustalw/
bioweb.pasteur.fr/seqanal/interfaces/clustalw.html

Phylodendrogram
PHYLIP evolution.genetics.washington.edu/phylip.html
njplot http://pbil.univ-lyon1.fr/software/njplot.html
MEGA http://www.megasoftware.net/

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/