Useful web resources

These web resources may prove useful to On-line Tutorial users. Inclusion in this list does not constitute an endorsement of the site by BayGenomics or guarantee its availability.

Alignments

pairwise alignments

BLAST 2 SEQUENCE - NCBI

http://www.ncbi.nlm.nih.gov/blast/bl2seq/wblast2.cgi
lalign and prss Swiss Institute for Experimental Cancer Research (ISREC)

http://www.isrec.isb-sib.ch/experiment/ALIGN_form.html
Pairwise Sequence Alignment - Michigan Technological Univ.

http://genome.cs.mtu.edu/align/align.html
SIM Alignment Tool - Protein Sequences (Expasy - Switzerland)

http://www.expasy.org/tools/sim-prot.html
mirror sites (these come and go, check the Swiss site for the latest list:
USA
http://us.expasy.org/tools/sim-prot.html
multiple alignments

clustalw:

EBI site

http://www.ebi.ac.uk/clustalw/
EMBnet site

http://www.ch.embnet.org/software/ClustalW.html
multalin:

multalin site
http://www.toulouse.inra.fr/multalin.html

multiple alignment visualization


boxshade server

http://www.ch.embnet.org/software/BOX_form.html
ESPript 2.0 server
http://prodes.toulouse.inra.fr/ESPript/cgi-bin/nph-ESPript_exe.cgi

Database searching

NCBI's BLAST tools
http://www.ncbi.nlm.nih.gov/blast/
FASTA - Univ. of Virginia

http://fasta.bioch.virginia.edu/fasta_www2/fasta_www.cgi?rm=select

Hydropathic Profile determination

Hydropathy/Secondary-Structure/seg - Univ. of Virginia

http://fasta.bioch.virginia.edu/fasta_www2/fasta_www.cgi?rm=misc1
Plot the Hydropathic Profile of a Protein Weizmann Institute of Science Genome and Bioinformatics

http://bioinformatics.weizmann.ac.il/hydroph/plot_hydroph.html

Modelling resources

DOCK

http://dock.compbio.ucsf.edu
DSSP database

http://www.cmbi.kun.nl/swift/dssp/
EBI MaxSprout

http://www.ebi.ac.uk/maxsprout
FLEXX

http://www.biosolveit.de/FlexX/
Model Evaluation site

http://biotech.ebi.ac.uk:8400/
Prosa II site

http://www.came.sbg.ac.at/Services/prosa.html
SCWRL

http://dunbrack.fccc.edu/SCWRL3.php
Swiss-Model

http://www.expasy.org/swissmod/SWISS-MODEL.html

Motif and Profile searching

input is a single sequence

Blocks Searcher Fred Hutchinson Cancer Research Center, Seattle

http://blocks.fhcrc.org/blocks/blocks_search.html
FPScan PRINTS scan with a protein sequence

http://umber.sbs.man.ac.uk/cgi-bin/dbbrowser/fingerPRINTScan/muppet/FPScan.cgi
Frame-ProfileScan server short DNA sequence against protein database (ISREC)

http://www.isrec.isb-sib.ch/software/PFRAMESCAN_form.html
PANAL Univ. of Minnesota

http://analysis.ccgb.umn.edu/panal/index.html
prosite patterns

http://www.expasy.org/tools/scanprosite
mirror sites (these come and go, check the Swiss site for the latest list:
USA
http://us.expasy.org/tools/scanprosite/
profilescan server prosite profiles (ISREC)

http://myhits.isb-sib.ch/cgi-bin/motif_scan

input is meme generated pattern

mast page

http://meme.sdsc.edu/meme/website/mast.html
mast intro

http://meme.sdsc.edu/meme/website/mast-intro.html

motif development

input is a series of related sequences

meme page [results via email]

http://meme.sdsc.edu/meme/website/meme.html
meme intro

http://meme.sdsc.edu/meme/website/meme-intro.html
pratt site Univ. of Bergen, Norway

http://www.ii.uib.no/~inge/Pratt.html

NCBI resources

documentation

Accession number

http://www.ncbi.nlm.nih.gov/Sitemap/samplerecord.html#AccessionB
BLAST substitution matrices

http://www.ncbi.nlm.nih.gov/BLAST/html/sub_matrix.html
dbEST summary

http://www.ncbi.nlm.nih.gov/dbEST/dbEST_summary.html
Fasta Format description

http://www.ncbi.nlm.nih.gov/BLAST/fasta.shtml
Genbank sample record

http://www.ncbi.nlm.nih.gov/Sitemap/samplerecord.html
GI number

http://www.ncbi.nlm.nih.gov/Sitemap/samplerecord.html#GInB
High Throughput Genomic Sequences

http://www.ncbi.nlm.nih.gov/HTGS/
Molecule type

http://www.ncbi.nlm.nih.gov/Sitemap/samplerecord.html#MoleculeTypeB
Reference Sequences

http://www.ncbi.nlm.nih.gov/RefSeq/
Version number

http://www.ncbi.nlm.nih.gov/Sitemap/samplerecord.html#VersionB
servers

BLAST 2 SEQUENCE

http://www.ncbi.nlm.nih.gov/blast/bl2seq/wblast2.cgi
NCBI's BLAST tools

http://www.ncbi.nlm.nih.gov/blast/
CD-Search

http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi
Entrez search

http://www.ncbi.nlm.nih.gov/Entrez/
Entrez Gene search

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene
OMIM search

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=OMIM

Protein family and Domain searching

CD-Search - NCBI [Cn3D viewer needed to display structures]
http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi
pfam sites:

Sanger Centre,
http://www.sanger.ac.uk/Software/Pfam/search.shtml
Washington Univ.

http://pfam.wustl.edu/hmmsearch.shtml
Prodom page

http://prodes.toulouse.inra.fr/prodom/doc/prodom.html
SMART page

http://smart.embl-heidelberg.de/

Secondary Structure prediction

Chou-Fasman and Garnier-Osguthorpe-Robson Secondary Structure Prediction

http://fasta.bioch.virginia.edu/fasta_www2/fasta_www.cgi?rm=misc1
GOR Secondary Structure Prediction

http://abs.cit.nih.gov/gor/
NNPREDICT Protein Secondary Structure Prediction

http://www.cmpharm.ucsf.edu/~nomi/nnpredict.html
PredictProtein server

http://cubic.bioc.columbia.edu/predictprotein/

Software

software distribution sites

clustalw

Clustalw EMBL molecular biology distribution site (pick platform)

ftp://ftp.ebi.ac.uk/pub/software
GeneDoc

GeneDoc download page

http://www.psc.edu/biomed/genedoc/gddl.htm
tree visualization software

Treeview download site
http://taxonomy.zoology.gla.ac.uk/rod/treeview.html
visualization software

Chime download

http://www.mdli.com/downloads/downloadable
Chimera download

http://www.cgl.ucsf.edu/chimera/download.html
CN3D download

http://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3dinstall.shtml
Mage download

http://kinemage.biochem.duke.edu/software/mage.php
Rasmol download

http://www.umass.edu/microbio/rasmol/getras.htm
Rasmol 2.7.2.1 site

http://www.bernstein-plus-sons.com/software/RasMol_2.7.2.1/README.html#CodeAndBinaries
Swiss-PDB Viewer download

http://www.expasy.org/spdbv/
mirror sites (these come and go, check the Swiss site for the latest list):
USA
http://us.expasy.org/spdbv/

software documentation

Rasmol 2.6

http://www.umass.edu/microbio/rasmol/distrib/rasman.htm

Structural databases

Dali database

http://ekhidna.biocenter.helsinki.fi/dali/start
FSSP database

http://ekhidna.biocenter.helsinki.fi/dali/start
ModBase database

http://alto.compbio.ucsf.edu/modbase-cgi/index.cgi
NDB database

http://ndbserver.rutgers.edu/
PDB database

http://www.rcsb.org/pdb/

Translation [DNA to protein]

Transeq EBI

http://www.ebi.ac.uk/emboss/transeq/
Translate Tool (Expasy - Switzerland)

http://www.expasy.org/tools/dna.html
mirror sites (these come and go, check the Swiss site for the latest list):
USA
http://us.expasy.org/tools/dna.html

Transmembrane prediction

DAS - Stockholm University

http://www.sbc.su.se/~miklos/DAS/
HMMTOP - Hungarian Academy of Sciences

http://www.enzim.hu/hmmtop/
MEMSAT2 - results via email - University College London

http://bioinf.cs.ucl.ac.uk/psipred/
PHDhtm - results via email -Columbia University - PredictProtein

http://cubic.bioc.columbia.edu/predictprotein/submit_adv.html#top
PRED - TMR - University of Athens, Greece

http://o2.biol.uoa.gr/PRED-TMR/
PRED - TMR2 - University of Athens, Greece

http://o2.biol.uoa.gr/PRED-TMR2/
Sosui - Tokyo University of Agriculture and Technology, Japan

http://sosui.proteome.bio.tuat.ac.jp/sosuiframe0.html
Split - University of Split, Croatia

http://split.pmfst.hr/split/4/
TMAP single - Karolinska Institutet, Sweden

http://www.mbb.ki.se/tmap/single.html
TMHMM - CBS: Denmark

http://www.cbs.dtu.dk/services/TMHMM-2.0/
TMpred - EMBnet-CH

http://www.ch.embnet.org/software/TMPRED_form.html
TSEG - results returned via email - Daisuke Kihara, Doctoral Student, Institute for Chemical Research, Kyoto University, Japan

http://www.genome.jp/SIT/tsegdir/tseg_exe.html

Transmembrane prediction display

TOPO2 - University of California, San Francisco

http://www.sacs.ucsf.edu//TOPO2/

Last updated 3/21/05