Bioinformatics Related Sites

　

Alignment Database

GenBank (NCBI)
EBI-EMBL
DDBJ DNA Data Bank of Japan
PIR Protein Information Resources (National Biomedical Research Foundation, Georgetown Univ. Medical Center)
SwissProt （ISREC）
SRS Sequence Retrieval System (EBI)

Bayesian Bioinformatics Program (Bioinformatics Laboratory of  Wadsworth Center)
BCM Search Launcher (Baylor College of Medicine
Human Genome Sequencing Center, One Baylor Plaza, Houston, TX)
SIM (Local Similarity Program）
Pairwise Sequence Alignment Program（GAP，NAP） (Sequence Analysis Server at Michigan Tech)
FASTA Program (Univ. of Virginia)
BLAST 2 SEQUENCES（BLASTN，BLASTP） (NCBI)
Likelihood-weighted Sequence Alignment for Protein 

　

XML Central of DDBJ http://xml.nig.ac.jp　
GRID http://www.globalgridforum.org/

　
DDBJ http://www.ddbj.nig.ac.jp　
DDBJ/GenBank/EMBL Feature Table Definition http://www.ddbj.nig.ac.jp／FT／full_index.html
Agent to help microbial information integration（AHMII） http://wdcm.nig.ac.jp/AHMII/ahmii.html
SRS http://srs.ddbj.nig.ac.jp/index.html
　
EMBL-EBI Biocatalog http://www.ebi.ac.uk/biocat/index.html
CRUSTALX ftp://ftp-igbmc.u-strasbg.fr/pub/ClustalX/
Se-Al http://evolve.zoo.ox.ac.uk/software/Se-Al/main.html
SeqPub http://iubio.bio.indiana.edu/IUBio-Software+Data/molbio/seqpup/
BioEdit http://www.mbio.ncsu.edu/BioEdit/bioedit.html
GeneDoc http://www.psc.edu/biomed/genedoc/
Seaview ftp://biom3.Univ-lyon1.fr/pub/mol_phylogeny/seaview
　
Applied Biosystems http://www.appliedbiosystems.co.jp/website/jp/biobeat/top.jsp
Tree View http://taxonomy.zoology.gla.ac.uk/rod/treeview.html
CLUSTALW ftp://ftp.ebi.ac.uk/pub/software/
DendroMaker for Macintosh http://www.cib.nig.ac.jp/dda/timanish/dendromaker/home-j.html
　
ScanProsite http://kr.expasy.org/tools/scnpsit1.html
ExPASy Proteomics tools http://kr.expasy.org/tools/
InterPro http://www.ebi.ac.uk/interpro/
　
RCSB  http://www.rcsb.org/
EBI  http://www.ebi.ac.uk/
PDB(Osaka Univ.) http://pdb.protein.osaka-u.ac.jp/
Entrez http://ncbi.nlm.nih.gov/Entrez
PDB  http://pdb.protein.osaka-u.ac.jp/pdb/index.html
PDB tutorial http://pdb.protein.osaka-u.ac.jp/pdb/query_tut.html
PDB software http://www.rcsb.org/pdb/software-list.html
PDB content guide http://pdb.protein.osaka-u.ac.jp/pdb/docs/format/pdbguide2.2/guide2.2_frame.html
PDB link http://pdb.protein.osaka-u.ac.jp/pdb/links.html
RasMol http://www.umass.edu/microbio/rasmol/
http://www.bernstein-plus-sons.com/software/rasmol/
MolScript http://www.avatar.se/molscript/
MolScript http://www.avatar.se/molscript/obtain_info.html
MolScript Installation http://www.avatar.se/molscript/doc/installation.html
MolScript v2.1 http://www.avatar.se/molscript/doc/molscript.html
MolAuto http://www.avatar.se/molscript/doc/molauto.html
OpenGL http://www.opengl.org/
BobScript http://www.strubi.ox.ac.uk/bobscript/
Raster3D http://www.bmsc.washington.edu/raster3d/raster3d.html
　
GTOP http://spock.genes.nig.ac.jp/~genome/gtop.html
Pfam sanger center http://www.sanger.ac.uk/Software/Pfam/
Pfam washington univ. http://pfam.wustl.edu/
Pfam http://pfam.jouy.inra.fr/
ProDom http://protein.toulouse.inra.fr/prodom/doc/prodom.html
SMART http://smart.embl-heidelberg.de/
PRINTS http://www.bioinf.man.ac.uk/dbbrowser/PRINTS/
Blocks http://blocks.fhcrc.org/
InterPro http://www.ebi.ac.uk/interpro/scan.html
CD-Search http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml
　
SCOP http://scop.mrc-lmb.cam.ac.uk/scop/index.html
CATH http://www.biochem.ucl.ac.uk/bsm/cath_new/index.html
Dali Domain Dictionary http://www2.ebi.ac.uk/dali/domain/3.0/
Dali server http://www.embl-ebi.ac.uk/dali/
FSSP http://www2.ebi.ac.uk/dali/fssp/fssp.html
CE http://cl.sdsc.edu/ce.html
VAST http://www.ncbi.nlm.nih.gov/Structure/VAST/vast.shtml
VAST Search http://www.ncbi.nlm.nih.gov/Structure/VAST/vastsearch.html
　
PHD http://cubic.bioc.columbia.edu/predictprotein/
PSIPRED http://bioinf.cs.ucl.ac.uk/psipred/
PREDATOR http://bioweb.pasteur.fr/seqanal/interfaces/predator.html
Jpred2 http://jpred.ebi.ac.uk
　
3D-PSSM http://www.sbg.bio.ic.ac.uk/~3dpssm/
FFAS http://bioinformatics.ljcrf.edu/FFAS/
GenTHREADER http://bioinf.cs.ucl.ac.uk/psipred/
FUGUE http://www-cryst.bioc.cam.ac.uk/~fugue/prfsearch.html
LIBRA http://www.ddbj.nig.ac.jp/E-mail/libra/LIBRA_I.html
　
ORF Finder http://www.ncbi.nlm.nih.gov/gorf/gorf.html
BLAST http://www.ncbi.nlm.nih.gov/BLAST/
http://blast.wustl.edu/
GeneMarkS http://opal.biology.gatech.edu/GeneMark/
Ensembl http://www.ensembl.org/
RepeatMasker http://ftp.genome.washington.edu/RM/RepeatMasker.html
MaskerAid http://sapiens.wustl.edu/maskeraid/
est2genome http://www.uk.embnet.org/Software/EMBOSS/Apps/est2genome.html
GLASS/Rosetta http://crossspecies.lcs.mit.edu/
Wise2 http://www.sanger.ac.uk/Software/Wise2/
PROCRUSTES http://www-hto.usc.edu/software/procrustes/wwwserv.html
ｓim4 http://globin.cse.psu.edu/globin/html/docs/sim4.html
GeneMark.hmm http://genemark.biology.gatech.edu/GeneMark/
GLIMMER http://www.tigr.org/software/glimmer/
FGENESH http://genomic.sanger.ac.uk/gf/gf.shtml
GENSCAN http://genes.mit.edu/GENSCAN.html
GenomeScan http://genes.mit.edu/genomescan/
TWINSCAN http://genes.cs.wustl.edu/
　
KEGG:Kyoto Encyclopedia of Genes and Genomes http://www.genome.ad.jp/kegg/
KEGG microarray http://www.genome.ad.jp/kegg/expression/
EcoCyc:Encyclopedia of E. coli Genes and Metabolism/MetaCyc:Metabolic Encyclopedia http://www.biocyc.org/
UM-BBD:Biocatalysis/Biodegradation Database http://umbbd.ahc.umn.edu/
UM-BBD http://umbbd.ahc.umn.edu/meta/meta_map.html
WIT:What IS There/EMP:Metabolic Pathway Database　 http://wit.mcs.anl.gov/WIT2/
http://emp.mcs.anl.gov/
Boehringer Mannheim:Biochemical Pathways http://www.expasy.ch/cgi-bin/search-biochem-index
Boehringer Mannheim:Biochemical Pathways http://www.expasy.ch/cgi-bin/show_thumbnails.pl
PathDB http://www.ncgr.org/pathdb/
BRITE:Biomolecular Relations in Information Transmission and Expression http://www.genome.ad.jp/brite/
CSNDB:Cell Signaling Networks Database http://geo.nihs.go.jp/csndb/
DIP:Database of Interacting Proteins http://dip.doe-mbi.ucla.edu/
GeNet:Gene Network Database http://www.csa.ru/Inst/gorb_dep/inbios/genet/genet.htm
Interactive Fly http://sdb.bio.purdue.edu/fly/aimain/1aahome.htm
SPAD:Signaling Pathway Database http://www.grt.kyushu-u.ac.jp/spad/
　
LIPIDBANK for Web http://lipid.bio.m.u-tokyo.ac.jp/
　
SAKURA http://sakura.ddbj.nig.ac.jp/
PDB ADIT http://pdbdep.protein.osaka-u.ac.jp/adit/
PubMed http://www.ncbi.nlm.nih.gov/PubMed/
PDBj http://pdbj.protein.osaka-u.ac.jp/

　

　

ClustalW or ClustalX ftp://ftp.ebi.ac.uk/pub/software/a,b

MSA		 http://www.psc.edu/b
http://www.ibc.wustl.edu/ibc/msa.htmlc
ftp://fastlink.nih.gov/pub/msa/
PRALINE http://mathbio.nimr.mrc.ac.uk/~jhering/praline/
DIALIGN http://www.gsf.de/biodv/dialign.html
MultAlin http://protein.toulouse.inra.fr/multalin.html
PRRP ftp://ftp.genome.ad.jp/pub/db/hgc/software/saitama-cc/
SAGA Sequence Alignment by Genetic Algorithm http://igs-server.cnrs-mrs.fr/~cnotred/Projects_home_page/saga_home_page.html
Asset（Aligned Segment Statistical Evaluation Tool） ftp://ncbi.nlm.nih.gov/pub/neuwald/asset/
BLOCKS (Fred Hutchinson Cancer Research Center) http://blocks.fhcrc.org/blocks/
eMOTIF (Stanford Univ.) http://dna.Stanford.EDU/emotif/
GIBBS ftp://ncbi.nlm.nih.gov/pub/neuwald/gibbs9_95/
HMMER Hidden Markov models (Washington Univ. in St.Louis) http://hmmer.wustl.edu/
MACAW（a workbench for multiple alignment construction and analysis） ftp://ncbi.nlm.nih.gov/pub/macaw/
MEME/MAST system http://meme.sdsc.edu/meme/website/
Profile analysis (SDSC) http://www.sdsc.edu/projects/profile/
SAM Sequence Alignment and Modeling System(UCSC) http://www.cse.ucsc.edu/research/compbio/sam.html

　


5S Ribosomal RNA Database http://biobases.ibch.poznan.pl/5SData
The Comparative RNA Web Site http://www.rna.icmb.utexas.edu/
GenLang :syntactic pattern recognition system http://www.cbil.upenn.edu/genlang/genlang_home.html
GOBASE organelle genome database http://alice.bch.umontreal.ca/genera/gobase/gobase.html

Ares lab Yeast Intron Database

 http://www.cse.ucsc.edu/research/compbio/yeast_introns.html
PLMItRNA :higher plant mitochondrial tRNA genes ftp://ftp.ebi.ac.uk/pub/databases/plmitrna/
mfold http://www.bioinfo.rpi.edu/applications/mfold/old/rna/form1.cgi
NDB Nucleic Acid Database Project http://ndbserver.rutgers.edu/
PseudoBase (Leiden Univ.) http://wwwbio.leidenuniv.nl/~batenburg/pkb.html
RNase P Database http://jwbrown.mbio.ncsu.edu/RNaseP/home.html
RDP The Ribosomal Database Project II http://rdp.cme.msu.edu
Ribosomal RNA Mutation Databases (16SMDBexp and 23SMDBexp) http://www.fandm.edu/Departments/Biology/Databases/RNA.html
 The RiboWeb Project http://www-smi.stanford.edu/projects/helix/ribo3dmodels/index.html
Aptamer Database (Univ. of Texas) http://aptamer.icmb.utexas.edu
RNA Editing Web Site (UCLA) http://www.lifesci.ucla.edu/RNA/index.html
　
Uridine insertion/deletion RNA Editing http://www.lifesci.ucla.edu/RNA/trypanosome/
The RNA Modification Database http://medlib.med.utah.edu/RNAmods/
The RNA Comparative Web Site http://www.rna.icmb.utexas.edu/
RNABase : RNA Structure Database http://www.rnabase.org/
The RNA World Website (IMB Jena) http://www.imb-jena.de/RNA.html
the European ribosomal RNA website (University of Gent) http://oberon.rug.ac.be:8080/rRNA
SRPDB (Signal Recognition Particle Database) http://psyche.uthct.edu/dbs/SRPDB/SRPDB.html
Small RNA Database http://mbcr.bcm.tmc.edu/smallRNA/smallrna.html
snoRNA Database (Washington Univ. in St.Louis) http://rna.wustl.edu/snoRNAdb/
tmRDB (tmRNA Database) http://psyche.uthct.edu/dbs/tmRDB/tmRDB.html
The tmRNA Website
 http://www.indiana.edu/~tmrna/
tRNAscan-SE Server (Washington Univ. in St.Louis) http://www.genetics.wustl.edu/eddy/tRNAscan-SE/
Compilation of tRNA sequences and sequences of tRNA genes http://www.uni-bayreuth.de/departments/biochemie/sprinzl/trna/
the uRNA Database http://psyche.uthct.edu/dbs/uRNADB/uRNADB.html
Vienna RNA Package (Institut für theoretische Chemie, Währingerstr) http://www.tbi.univie.ac.at/~ivo/RNA/