Download To on your computer

Resources
Databases links
We have been teaching workshops for several years with a resource page found Here . (It
might not be totally up to date but it is still useful.) Here is another list of Bioinformatic
resources for biologists that I like: http://molbiol-tools.ca .
Below is a list we try and keep up to date and that lists many of the sites we use in class.
General databases
EBI:
http://www.ebi.ac.uk
NCBI Gquery: http://www.ncbi.nlm.nih.gov/gquery/
Entrez help
fields: http://www.ncbi.nlm.nih.gov/entrez/query/static/help/Summary_Matrices.html : http://w
ww.ncbi.nlm.nih.gov/entrez/query/static/help/Summary_Matrices.html (Links to an external sit
NCBI ressources: http://www.ncbi.nlm.nih.gov/guide/all/#howto
NAR database : http://www.oxfordjournals.org/nar/database/c/
UniProt SwissProt: http://www.uniprot.org/
BioCyc: http://biocyc.org ( note subscription needed for some features)
Organisms specific databases
SGD: http://www.yeastgenome.org/
Ecogene: http://www.ecogene.org
TAIR: http://www.arabidopsis.org/
Pseudomonas database GB: http://www.pseudomonas.com
EcoCyc: http://ecocyc.org
Databases related to enzymes and Pathways
Enzyme nomenclature database: http://www.expasy.org/enzyme/
BRENDA: http://www.brenda-enzymes.org/
KEGG: http://www.kegg.jp/kegg/pathway.html
Structures, PDB :
http://www.rcsb.org/
Visualizing pathways, mapping data to pathways, metabolic reconstruction
MetaCyc: http://metacyc.org/
iPAth: http://pathways.embl.de/
ModelSEED: Link http://seed-viewer.theseed.org/seedviewer.cgi?page=ModelView
Reactome (eukaryotes only): http://www.reactome.org/ (Links to a
Practical tools
Gene Infinity: http://geneinfinity.org/
Omics Tools: https://omictools.com
ReadSeq 1, change format tool: http://www-bimas.cit.nih.gov/molbio/readseq/
Seqret, change format tool: http://www.ebi.ac.uk/Tools/sfc/emboss_seqret/
SeqMassager, Sequence clean up tool:
http://www.attotron.com/cybertory/analysis/seqMassager.htm
Reverse complement DNA: http://www.bioinformatics.org/sms/rev_comp.html
Bionumbers: http://www.bionumbers.hms.harvard.edu/ ( all types of numbers related to
Biology)
VENNY: http://bioinfogp.cnb.csic.es/tools/venny/index.html ( VENN Diagram tools)
Alignment tools
Aligning two sequences
Align two sequences of DNA: http://www.bioinformatics.org/sms2/pairwise_align_dna.html
Align two sequences of Proteins :
http://www.bioinformatics.org/sms2/pairwise_align_protein.html
Align 2 proteins with Blast:
http://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastSearch&BLAST_SPEC=blast2seq&
LINK_LOC=align2seq
Dotplot site 1, DotLet: http://myhits.isb-sib.ch/cgi-bin/dotlet
Dotlet help: http://myhits.isb-sib.ch/util/dotlet/doc/dotlet_help.html
Doptplot site 2 : http://www.genebee.msu.su/services/dhm/advanced.html
Compare two genomes: https://genomevolution.org/CoGe/SynMap.pl
Smith-Waterman full-length alignments between two sequences:
http://pir.georgetown.edu/pirwww/search/pairwise.shtml
Pearson alignment method between two proteins, LALIGN:
http://www.ch.embnet.org/software/LALIGN_form.html
PRSS3 - evaluates the significance of a protein sequence alignment:
http://www.ch.embnet.org/software/PRSS_form.html
Database searches
Blast@NCBI: https://blast.ncbi.nlm.nih.gov/Blast.cgi
ConciseBlast, blasts a reduced database from protein clusters :
http://www.ncbi.nlm.nih.gov/genomes/prokhits.cgi
Useful tool to find similar DNA regions in human genome, BLAT : http://genome.ucsc.edu/cgibin/hgBlat?hgsid=412713987_NrFiBsC7HAfLzfiAeKNgr11VBglP&command=start
Sequence similarity searches@EBI includes FASTA : http://www.ebi.ac.uk/Tools/sss/
Exhaustive database search, SCANPS: http://www.compbio.dundee.ac.uk/www-scanps
Blast Pubmed1, Seq2ref: http://prodata.swmed.edu/seq2ref/
Blast Pubmed2, PubServer: http://pubserver.burnham.org/
Blast@KEGG: http://www.genome.jp/tools/blast/
Multiple sequence alignments
CustalOmega: http://www.ebi.ac.uk/Tools/msa/clustalo/
T-coffee: http://tcoffee.crg.cat/apps/tcoffee/index.html
Multialin: http://multalin.toulouse.inra.fr/multalin/
Visualize alignments: http://www.ebi.ac.uk/Tools/msa/mview/
Compilation of MSA programs @EBI
http://www.ebi.ac.uk/Tools/msa/
Platform to run different alignment programs ( signing up allows to save your work)
http://mobyle.pasteur.fr/cgi-bin/portal.py#welcome
Motifs and Protein domains
Motifs
Prosite: http://www.expasy.ch/prosite/
Meme: http://meme-suite.org
Logo builder Weblogo: http://weblogo.threeplusone.com
Comapre Logos, Two Sample Logo: http://www.twosamplelogo.org/cgi-bin/tsl/tsl.cgi
Protein domains
Pfam: http://pfam.xfam.org
NCBI CDD/ CDART: http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml
CDD Search: http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi
Interpro: http://www.ebi.ac.uk/interpro/
ProDom: http://prodom.prabi.fr/prodom/current/html/home.php
Genome Protmap, maps proteins families in contigs:
http://www.ncbi.nlm.nih.gov/sutils/protmap.cgi
Good compilation of protein MSA domain and signature sites: https://npsa-prabi.ibcp.fr/cgibin/npsa_automat.pl?page=/NPSA/npsa_server.html
Structure based domains @ SCOP :http://scop.mrc-lmb.cam.ac.uk/scop/
Structure based domains @ SCOP2: http://scop2.mrc-lmb.cam.ac.uk
Structure based domains @CATH :
http://www.cathdb.info/
Genome browsers within integrated platforms
SEED viewer: http://pubseed.theseed.org/
IMG-JGI: https://img.jgi.doe.gov/cgi-bin/w/main.cgi
UCSC Archaeal GB : http://archaea.ucsc.edu/
Microscope: https://www.genoscope.cns.fr/agc/microscope/home/index.php
Pseudomonas database GB: http://www.pseudomonas.com/gbrowse_index.jsp
UCSC Human GB: http://genome.ucsc.edu/cgi-bin/hgGateway
Mapviewer, advanced browsing for a subset of genomes@NCBI :
http://www.ncbi.nlm.nih.gov/projects/mapview/
Yeast SGD GB: GO TO Sequence/browser @SGD
Eukaryotic GB at e!Ensembl : http://useast.ensembl.org/index.html
Prokaryotic GB b!Ensembl: http://bacteria.ensembl.org/index.html
Island Viewer: http://www.pathogenomics.sfu.ca/islandviewer/browse/
Genome Projector http://www.g-language.org/GenomeProjector/
Gene finders
tRNA-scan: http://lowelab.ucsc.edu/tRNAscan-SE/
rRNA-finder : http://www.cbs.dtu.dk/services/RNAmmer/
NCBI-ORF Finder: http://www.ncbi.nlm.nih.gov/gorf/orfig.cgi
GeneMark, a family of programs to predict genes: http://exon.biology.gatech.edu/GeneMark/
tRNA database: http://lowelab.ucsc.edu/GtRNAdb/
Plant genome databases
Arabidopsis, TAIR: https://www.arabidopsis.org/
Maize, Gramene: http://ensembl.gramene.org/Zea_mays/Info/Index
Maize, GDB: http :// www.maizegdb.org
All plants: http://www.gramene.org/
The viridiplantae branch @ http://genome.jgi-psf.org/
PlantSEED: http://bioseed.mcs.anl.gov/~seaver/FIG/seedviewer.cgi?page=PlantSEED
PlantGDB: http://www.plantgdb.org/
DNA motif finders or databases
Bacterial ressources
Bacterial sRNA target predictor: http://rna.tbi.univie.ac.at/RNApredator2/target_search.cgi
Prokaryotic regulatory site compilation REGPrecise: http://regprecise.lbl.gov/RegPrecise/
Regulon DB: http://regulondb.ccg.unam.mx /
CollecTF: http://collectf.umbc.edu/browse/home/
Prokaryotic gene regulation database: http://www.prodoric.de/
Platform to predict regulatory sites in Bacteria RegPredict: http://regpredict.lbl.gov/regpredict/
Motif finding platform MEME: http://meme-suite.org
Riboswitch Finder : http://132.248.32.45/cgi-bin/ribex.cgi
RNAfam ( contains riboswitches): http://rfam.xfam.org/
Regulatory overview of E. coli: http://www.ecocyc.org/overviewsWeb/regOv.shtml
General gene finding and promoter finding tools in prokaryotes and eukaryotes:
http://linux1.softberry.com/berry.phtml
Eukaryotic ressources
Plant promoter database: http://ppdb.agr.gifu-u.ac.jp/ppdb/cgi-bin/index.cgi
Plant Transcription factor databases:
http://planttfdb.cbi.pku.edu.cn/
http://plntfdb.bio.uni-potsdam.de/v3.0/
Human Transcriptional Regulatory Element Database: https://cb.utdallas.edu/cgibin/TRED/tred.cgi?process=home
Coexpression database: http://coxpresdb.jp/
Cloning tools platforms
Restriction mapping: http://nc2.neb.com/NEBcutter2/
Primer Design, primer 3: http://frodo.wi.mit.edu/primer3/
Primer Blast: http://www.ncbi.nlm.nih.gov/tools/primer-blast/
Primer design Primer3plus:http://www.bioinformatics.nl/cgi-bin/primer3plus/primer3plus.cgi
Free in silico cloning platform, ApE: http://biologylabs.utah.edu/jorgensen/wayned/ape/
Free in silico cloning platform, Serial Cloner: http://serialbasics.free.fr/Serial_Cloner.html
Physical and chemical properties of a protein@Expasy: http://web.expasy.org/protparam/
Electronic notebook plasmid depository: https://benchling.com/academic
Plasmid depository: https://www.addgene.org/
https://benchling.com/academichttps://benchling.com/academic
Protein analysis tools
Compilation of protein analysis tools@ Expasy: http://www.expasy.org/proteomics
Compilation of protein analysis tools @ CBS : http://www.cbs.dtu.dk/services/
Compute PI/MW@expasy: http://web.expasy.org/compute_pi/
Find a protein sequence based on the AA composition@Expasy:
http://web.expasy.org/aacompident/
Calculate % identity similarities between proteins: http://imed.med.ucm.es/Tools/sias.html
Prediction of transmembrane helices, TMHMM: http://www.cbs.dtu.dk/services/TMHMM/
Signal sequence analysis, SignalP : http://www.cbs.dtu.dk/services/SignalP/
Signal Sequence analysis for Bacteria, Psort: http://www.psort.org/psortb/
Targeting prediction eukaryotes, TargetP: http://www.cbs.dtu.dk/services/TargetP/
Combined transmembrane and signal sequence, Phobius: http://phobius.sbc.su.se/
Plant Proteome database: http://ppdb.tc.cornell.edu/introduction.aspx
Plastid protein database: http://www.plprot.ethz.ch/
Mitominer: http://mitominer.mrc-mbu.cam.ac.uk/release-3.1/begin.do
Phylogeny tools
GENERAL BIOINFORMATIC PLATFORM WITH MANY PHYLOGENY TOOLS AND
PIPELINE: http://mobyle.pasteur.fr/cgi-bin/portal.py#welcome
Phylogeny platform Phylogeny.fr: http://www.phylogeny.fr
EBI Clustal Phylogeny tool: http://www.ebi.ac.uk/Tools/phylogeny/clustalw2_phylogeny/
Seaview platform: http://doua.prabi.fr/software/seaview
Mega platform: http://www.megasoftware.net/
PhyloDedron Phylogenetic tree printer: http://iubio.bio.indiana.edu/treeapp/treeprint-form.html
ITol (species trees and add data to trees): http://itol.embl.de/
Evolgenius: http://evolgenius.info/evolview/#login
Environment for Tree Exploration (ETE) http://etetoolkit.org /
Display and annotation of trees, ITOL: http://itol.embl.de
Structure visualization platforms
To download on your computer
Rasmol :http://www.umass.edu/microbio/rasmol/
Molscript : http://www.avatar.se/molscript/
Swiss-PDBViewer : http://spdbv.vital-it.ch/
Grasp : http://wiki.c2b2.columbia.edu/honiglab_public/index.php/Software:GRASP2
Chimera: http://www.cgl.ucsf.edu/chimera/
PyMol Educational Free but more limited version of Pymol and cannot be used for
research
http://pymol.org/edu/?q=educational/
Structure visualization on the web
Note: These can be seen on the web but require Java so you will need to most certainly add them
to your security settings
NCBI Cn3D - http://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3d.shtml ( you will need to
download Cn3D, but very easy)
PDB Jmol: http://jmol.sourceforge.net/
General Protein sequence analysis server with many 2D structures predictions tools;
http ://npsa-pbil.ibcp.fr/cgi-bin/npsa_automat.pl?page=/NPSA/npsa_server.html
Jpred4: http://www.compbio.dundee.ac.uk/jpred4
Web-based 3D structures prediction platforms
Phyre2: http://www.sbg.bio.ic.ac.uk/phyre2/html/page.cgi?id=index
SwissModel: https://swissmodel.expasy.org/interactive
Tasser: http://zhanglab.ccmb.med.umich.edu/I-TASSER/
Structural genomics
Structural genomics Knowledge base: http://kb.psi-structuralgenomics.org/
Structural genomics Target database: http://sbkb.org/tt/
UNKNOWN GENE/ENZYME DATABASES
ORENZA http://www.orenza.u-psud.fr/
orphan enzymes)
ORphan ENZyme Activities database (lists 1,200
ADOMETA http://vitkuplab.cu-genome.org/html/adometa/adometa.html ADoption of
Orphan METabolic Activities (Orphan enzyme activities in E. coli, B. subtilis, and S.
cerevisiae).
ORPHAN ENZYME PROJECT http://www.orphanenzymes.org/
GREP http://bisscat.org/GREP/ Generator of Reaction Equations & Pathways look for reported
and putative enzyme reaction equations, especially designed for finding metabolic pathways on
orphan metabolites (compounds known to be present at least in a living organism, but whose
synthetic/degradation pathways are unknown).
General integration platforms (genome browsers, genome comparisons (pathways or
synteny), phylogenetic distribution queries, physical clustering etc.)
SEED http://www.theseed.org/wiki/Main_Page Database containing hundreds of genomes
and many valuable tools.
SEED Subsystems http://pubseed.theseed.org//SubsysEditor.cgi Advanced comparative
genomic tools see
http://www.hos.ufl.edu/meteng/HansonWebpagecontents/workshop/NSF%20Maize%20Worksh
op.html for training
Patric http://www.patricbrc.org/ Emphasis on Pathogenic bacteria (but contains all sequenced
bacterial genomes), multiple tools
MicroScope https://www.genoscope.cns.fr/agc/microscope/home/index.php Microbial
genome annotation platform (Strong on metabolism)
MicrobesOnline: http://microbesonline.org
IMG http://img.jgi.doe.gov/ Integrated Microbial genomes data analysis system
IMG-JGI: https://img.jgi.doe.gov/cgi-bin/w/main.cgi
MGDB http://mbgd.genome.ad.jp/
Microbial Genome DataBase for comparative genomics.
MG-RAST http://metagenomics.anl.gov/ Depository and analysis of metagenomics data
EFI http://enzymefunction.org/ The Enzyme Function Initiative (EFI) is developing a robust
sequence / structure based strategy for facilitating discovery of in vitro enzymatic and in vivo
metabolic / physiological functions of unknown enzymes discovered in genome projects
Fusions. http://modelseed.org/projects/fusions/ Search for fusions.
Multiple Associations platforms
STRING http://string.embl.de/ Database of known and predicted protein-protein relationships,
derived from genomic context (fusions, conserved gene clusters, co-occurrence), high throughput
experiments (co-expression), and the literature. STRING quantitatively integrates data from
bacteria and other organisms.
STITCH http://stitch.embl.de/ STRING incorporating small molecules
eNet http://ecoli.med.utoronto.ca/ E. coli gene function prediction database integration of
microarray and protein interaction data.
EcoliNet: http://www.inetbio.org/ecolinet/ another database that integrates different types of
evidence for E. coli
GeneMania http://genemania.org very visual Data integration for a handful of model organisms
AraNet http://www.functionalnet.org/aranet/search.html Gene associations in Arabidopsis.
BioPixie: http://imp.princeton.edu intergration of data for a handful of eukaryotes nice graphics
DIP http://dip.doe-mbi.ucla.edu/dip/Main.cgi database of interacting proteins from different
organisms.
List of Pathways and interactions databases : http://pathguide.org/
ConsensusPath DB: http://cpdb.molgen.mpg.de/YCPDB for yeast/human/mouse
Phylogenetic distribution tools
JGI Phylogenetic Profiler http://img.jgi.doe.gov/cgibin/w/main.cgi?section=PhylogenProfiler&page=phyloProfileForm Phylogenetic Profiler for
Single Genes.
MicroScope Phyloprofile
Exploration https://www.genoscope.cns.fr/agc/microscope/compgenomics/phyloprofil.php?
MicrobesOnline Phyletic Pattern http://www.microbesonline.org/cgibin/matchphyloprofile.cgi
ORTHOMCL: http://orthomcl.org/orthomcl/ (great for eukaryotes)
Phenotype data
Yeast phenotype data: http://fitdb.stanford.edu/
E.coli phenotype data: http://ecoliwiki.net/tools/chemgen/
E. coli Biolog data: http://ecoli.naist.jp/GB/index.php/biolog
RAPID http://rarge.gsc.riken.jp/phenome/ RIKEN Arabidopsis Phenome Information
Database, phenotypic data in transposon-insertional mutants.
SeedGenes http://www.seedgenes.org/
mutation.
Genes that give a seed phenotype when disrupted by
GOLM Metabolome: http://gmd.mpimp-golm.mpg.de
MicrobesOnline http://www.microbesonline.org/ A comprehensive database that includes
correlated TnSeq data for four organisms
TnSeq Fitness Browser: http://fit.genomics.lbl.gov/cgi-bin/myFrontPage.cgi
ESSENTIAL GENES DATABASES (Pro- and Eukaryote)
OGEE http://ogeedb.embl.de/#summary Online GEne Essentiality database
DEG http://tubic.tju.edu.cn/deg/ or http://www.essentialgene.org/ Database of Essential Genes
MICROARRAY & RNASeq DATABASES AND ANALYSIS RESOURCES
General Depositories
GEO http://www.ncbi.nlm.nih.gov/geo/ Gene Expression Omnibus
ARRAY Express : http://www.ebi.ac.uk/arrayexpress/
Web-Based analysis of your own data
Gene pattern : http://genepattern.broadinstitute.org/gp/pages/index.jsf
Patric: RNA Seq analysis
Precomputed analysis of expression data
ATTED http://atted.jp/ A simple site to use to look for co-expression patterns in Arabidopsis; it
shows gene networks, not just lists of correlated genes.
COEXPRESdb http://coxpresdb.jp Co-expression in yeasts and animals.
COXPRESdb provides data for both S. cerevisiae and S. pombe, while Golm does cerevisae
only. COXPRESdb displays co-expression data for orthologs -when they exist- in invertebrates
and vertebrates. Such similar patterns of coexpression accross species can generate very strong
predictions.
FungiDB http://fungidb.org/fungidb/
Diurnal http://diurnal.mocklerlab.org/ Circadian/Diurnal gene expression data for an
individual or set of Arabidopsis, rice, or poplar genes
Translatome eFP
cell populations
http://efp.ucr.edu/
Transcriptome profiling of 13 discrete Arabidopsis
PLEXdb http://www.plexdb.org/ Plant Expression Database
Botany Array Resource http://bbc.botany.utoronto.ca/
electronic Northerns.
CyanoExpress http://cyanoexpress.sysbiolab.eu
sp. PCC 6803. Instructions:
Tools for finding co-responses,
Co-expression database for Synechocystis
1) On the homepage, click 'gene expression'
2) Click 'all perturbations'
3) In the blank field 'search for' on the upper left part of the page paste your gene id (e.g.
sll0635), click go
4) In the new page, click the microarray picture (a single band). A larger microarray image will
appear; there is a column on the right that lists your top 20 co-regulated genes (most of them
functionally annotated from the poorly maintained and obsolete Cyanobase).
MetaOmGraph http://metnetdb.org/MetNet_MetaOmGraph.htm
large datasets
Tool to plot and analyze
qteller http://qteller.com/ RNAseq data for maize, sorghum, rice. Simple tools for expression
in various organs, correlation of expression of two genes.

Bacteria
MicrobesOnline http://www.microbesonline.org/ A comprehensive database that includes
correlated gene expression in E. coli and other bacteria
EcoGene http://ecogene.org/ A rich resource on E. coli that includes Microarray data on the
major changes in gene expression observed in various experiments.
GenExpDB https://genexpdb.okstate.edu/?query=b0145 E. coli Community Gene Expression
DataBase
COLUMBO Platform: http://www.colombos.net ( expression data analysis for prokaryotes)
Porteco http://www.porteco.org/
phenotype data
E. coli microarray analysis they also have analysis of the
Patric http://www.patricbrc.org/ ( has integrated Expression data for many Bacteria)

Yeast
SPELL http://spell.yeastgenome.org/

Co-response search tool for yeast
Mammals
BioGPS
http://biogps.org/#goto=welcome
A Compilation : http://omictools.com/gene-expression-c878-p1.html

Painting data on pathways
BioCyc : http://biocyc.org
Paintomics: http://bioinfo.cipf.es/paintomics/
PRIMe http://prime.psc.riken.jp/ Server for metabolomics and transcriptomics, tools for
metabolomics, transcriptomics and integrated analysis of different omics data.

Heatmaps and PCA tools
ClustVis: http://biit.cs.ut.ee/clustvis/
WebMeV (Multiple Experiment Viewer): http://www.tm4.org/#/welcome
Comparative genomics tutorials
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


Methods Paper
Lecture 1: Predicting Gene Function by Comparative Genomics
Lecture 2: Using Comparative Genomics Resources
Lecture 3: Phylogenetic Distribution Tools