Difference between revisions of "Bioinformatics links"

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*[http://bioinformatics.ubc.ca/resources/links_directory/ Bioinformatics Links Directory]
 
*[http://bioinformatics.ubc.ca/resources/links_directory/ Bioinformatics Links Directory]
 +
 +
==Source material==
 +
*[http://www.ncbi.nlm.nih.gov/sites/entrez/ PubMed]
 +
**[http://openwetware.org/wiki/Hardcore_PubMeding_%28advanced_PubMed_searching%29 Hardcore PubMeding (advanced PubMed searching)]
 +
*[http://www.hubmed.org/ HubMed]
 +
*[http://www.pubmedreader.com/ PubMed Reader]
 +
*[http://www.authoratory.com/ Authoratory]
 +
 +
==Bioinformatics related blogs==
 +
*[http://wiki.nodalpoint.org/blogs Computational Biology - Bioinformatics Blogs] — long list of blogs
 +
*[http://www.postgenomic.com/ PostGenomic]
 +
*[http://binf.twoday.net/ Notes from the Biomass]
 +
*[http://www.ghastlyfop.com/blog/ Flags and Lollipops]
 +
*[http://bioblogs.wordpress.com/ Bio::Blogs]
 +
*[http://www.paraschopra.com/blog/biohacking.php BioHacking]
 +
*[http://lurena.vox.com/profile/ Systems Biology & Bioinformatics]
 +
*[http://www.rnabioinformatics.com/ RNA Bioinformatics]
 +
*[http://www.labaction.com/ LabAction] — Human Genetics,Science Projects,Science Experiments
 +
*[http://fungalgenomes.org/blog/ Fungal Genomes and Comparative Genomics]
 +
*[http://phylogenomics.blogspot.com/ The Tree of Life] — blog of Jonathan A. Eisen
 +
*[http://cyclotis.blogspot.com/ note2self]
 +
*[http://bmistudents.blogspot.com/ BMI Students]
 +
*[http://www.ghastlyfop.com/ Flags and Lollipops]
 +
*[http://www.eyeondna.com/ Eye on DNA]
  
 
==Databases==
 
==Databases==
Line 7: Line 31:
 
*[http://www.ncbi.nlm.nih.gov/ NCBI/GenBank (USA)] — offers many important databases (PubMed, GenBank, OMIM) and some tools.
 
*[http://www.ncbi.nlm.nih.gov/ NCBI/GenBank (USA)] — offers many important databases (PubMed, GenBank, OMIM) and some tools.
 
*[http://www.ddbj.nig.ac.jp/ DDBJ (Japan)]
 
*[http://www.ddbj.nig.ac.jp/ DDBJ (Japan)]
 +
*[http://www.crossref.org/ CrossRef]
  
 
===Genomes===
 
===Genomes===
Line 13: Line 38:
 
*[http://www.sanger.ac.uk/Projects/Microbes/ Sanger]
 
*[http://www.sanger.ac.uk/Projects/Microbes/ Sanger]
 
*[http://ncbi.nlm.nih.gov/Genomes/index.html NCBI]
 
*[http://ncbi.nlm.nih.gov/Genomes/index.html NCBI]
 +
*[http://genome.ucsc.edu/ENCODE/ UCSC ENCODE Project] (includes latest, most complete build of the Human genome)
  
===Lists of genomes in progress===
+
====Lists of genomes in progress====
 
*[[Genome projects]]
 
*[[Genome projects]]
 
*http://wit.integratedgenomics.com/GOLD/
 
*http://wit.integratedgenomics.com/GOLD/
Line 20: Line 46:
 
*[http://www.ensembl.org/info/data/download.html Ensembl genome download] (mainly Eukaryotes)
 
*[http://www.ensembl.org/info/data/download.html Ensembl genome download] (mainly Eukaryotes)
 
*[http://www.genomesonline.org/gold.cgi?want=Published+Complete+Genomes Complete Published Genome Projects: 524]
 
*[http://www.genomesonline.org/gold.cgi?want=Published+Complete+Genomes Complete Published Genome Projects: 524]
 +
 +
===Genes / Proteins===
 +
*[http://www.ncbi.nlm.nih.gov/sites/entrez?db=OMIM Online Mendelian Inheritance in Man (OMIM)
 +
*[http://www.anc.ed.ac.uk/mscs/PPID/ PPID - Protein to Protein Interaction Database]
 +
*[http://harvester.fzk.de/harvester/ Bioinformatic Harvester III (beta)]
 +
*[http://www.ihop-net.org/UniPub/iHOP/ iHOP - Information Hyperlinked over Proteins]
  
 
==Web servers==
 
==Web servers==
 
*[http://molvis.sdsc.edu/visres/servers/titles.jsp World Index of BioMolecular Visualization Resources]
 
*[http://molvis.sdsc.edu/visres/servers/titles.jsp World Index of BioMolecular Visualization Resources]
 
*[http://wwwmgs.bionet.nsc.ru/mgs/gnw/pdbsitescan/ PDBSiteScan]
 
*[http://wwwmgs.bionet.nsc.ru/mgs/gnw/pdbsitescan/ PDBSiteScan]
*[http://www.ebi.ac.uk/thornton-srv/databases/CSA/ Catalytic Site Atlas (CSA)] — a database documenting enzyme active sites and catalytic residues in enzymes of 3D structure.
 
*[http://bioinfo3d.cs.tau.ac.il/SiteEngine/ SiteEngine] — Functional Sites Structural Search Engine; Recognizes regions on the surface of one protein that resemble a specific binding site of another.
 
 
*[http://sumo-pbil.ibcp.fr/cgi-bin/sumo-welcome SuMo]
 
*[http://sumo-pbil.ibcp.fr/cgi-bin/sumo-welcome SuMo]
*[http://astral.berkeley.edu/ ASTRAL] — The ASTRAL Compendium for Sequence and Structure Analysis.
 
*[http://www.molmovdb.org/ MolMovDB] — Database of Macromolecular Movements with Associated Tools for Flexibility and Geometric Analysis.
 
 
*[http://scop.berkeley.edu/ SCOP: Structural Classification of Proteins]
 
*[http://scop.berkeley.edu/ SCOP: Structural Classification of Proteins]
 +
*[http://rna.tbi.univie.ac.at/cgi-bin/alifold.cgi Vienna RNA Secondary Structure Prediction]
 
*[http://wikiomics.org/wiki/Searching_for_3D_functional_sites_in_a_protein_structure Searching for 3D functional sites in a protein structure]
 
*[http://wikiomics.org/wiki/Searching_for_3D_functional_sites_in_a_protein_structure Searching for 3D functional sites in a protein structure]
 
*[[wikipedia:Structural genomics]]
 
*[[wikipedia:Structural genomics]]
 +
*[http://harvester.fzk.de/harvester/ Bioinformatic Harvester III (beta)]
 +
;[http://www.ebi.ac.uk/thornton-srv/databases/CSA/ Catalytic Site Atlas (CSA)] : a database documenting enzyme active sites and catalytic residues in enzymes of 3D structure.
 +
;[http://bioinfo3d.cs.tau.ac.il/SiteEngine/ SiteEngine] : Functional Sites Structural Search Engine; Recognizes regions on the surface of one protein that resemble a specific binding site of another.
 +
;[http://astral.berkeley.edu/ ASTRAL] : The ASTRAL Compendium for Sequence and Structure Analysis.
 +
;[http://www.molmovdb.org/ MolMovDB] : Database of Macromolecular Movements with Associated Tools for Flexibility and Geometric Analysis.
 +
;[http://ekhidna.biocenter.helsinki.fi/dali/start Dali Fold Classification] : based on exhaustive, all-against-all 3D structure comparison of protein structures in the Protein Data Bank
 +
;[http://www.ebi.ac.uk/thornton-srv/databases/pdbsum/ PDBsum] : provides an at-a-glance overview of every macromolecular structure deposited in the Protein Data Bank
 +
;[http://blocks.fhcrc.org/ BLOCKS] : a service for biological sequence analysis
 +
;[http://www.daimi.au.dk/%7Ecompbio/animators/index.html Animators] : Visualization tools for the Wright-Fisher model and continous time coalescent.
 +
;[http://www.daimi.au.dk/%7Ecstorm/combat/index.html CombAt] : Comparison of coding DNA that takes the encoded proteins into account.
 +
;[http://www.cbs.dtu.dk/services/distanceP/ distanceP] : Predict distance constraints between amino acids in proteins from the amino acid sequence.
 +
;[http://www.birc.au.dk/fabox FaBox] : FASTA online toolbox
 +
;[http://www.bioinf.au.dk/FOLDALIGN/ FOLDALIGN] : Find the most significant common sequence and structure motifs in a set of RNA sequences.
 +
;[http://cgi-www.daimi.au.dk/cgi-chili/GeMprospector/main GeMprospector] : Find cross-species genetic marker candidates online from a collection of plant ESTs.
 +
;[http://www.daimi.au.dk/%7Ecompbio/hudson/hudson.html Hudson] : Simulation of sequence evolution using the Hudson coalescent process to make a phylogony and the Jukes-Cantor      substitution process.
 +
;[http://www.cbs.dtu.dk/services/MatrixPlot/ MatrixPlot] : Generate mutual information plots of sequence alignments, distance matrices of sequence with known 3D coordinates,      and plots of user provided matrix files.
 +
;[http://cgi-www.daimi.au.dk/cgi-chili/phyfi/go Phy·fi] : Online tool for drawing Newick trees in color. Supports the JPG, GIF, PNG, TIF, PDF, and EPS formats.
 +
;[http://cgi-www.daimi.au.dk/cgi-chili/PriFi/main PriFi] : Suggest primer pairs based on a DNA sequence alignment and give an account of the quality of the suggested primers.
 +
;[http://www.daimi.au.dk/%7Ecompbio/recpars/recpars.html RecPars] : Phylogenetic analysis using a parsimony analysis that takes recombination events into account.
 +
;[http://www.daimi.au.dk/%7Ecompbio/rateshift/ Rateshift analysis] : Find signs of functional divergence as evidenced by shifts in evolutionary rates between two DNA, RNA or protein sub-families.
 +
;[http://www.retrosearch.dk RetroSearch] : Database of ORF annotated human endogenous retroviruses.
 +
;[http://www.bioinf.au.dk/rnadbtool/ RNA DB Tools] : Collection of tools which can be used to perform semi-automated update of RNA structural databases.
 +
;[http://www.daimi.au.dk/%7Ecompbio/rnafold/ RNA Folding] : Find common secondary structures for multiple RNA sequences.
 +
;[http://www.bioinf.au.dk/slash SLASH] : Stem-Loop Align SearcH. Search for a common stemloop motif in a relatively large data set.
 +
;[http://www.daimi.au.dk/%7Ecompbio/statal/statal.html StatAl] : Statistical alignment of DNA/protein sequences.
 +
;[http://psyche.uthct.edu/dbs/SRPDB/SRPDB.html SRPDB] : Signal recognition particle database.
 +
;[http://psyche.uthct.edu/dbs/tmRDB/tmRDB.html tmRDB] : tmRNA database ([http://www.bioinf.au.dk/tmRDB/])
 +
 +
==Downloadable Software==
 +
;[http://www.daimi.au.dk/%7Emailund/Blossoc/ Blossoc] : Block-Association Mapping.
 +
;[http://www.daimi.au.dk/%7Emailund/clustalw_wrapper.html ClustalW Wrapper] : The clustalw python module contains code for wrapping the ClustalW multiple sequence alignment tool. Bundled with the ClustalW wrapper is also modules for reading FASTA and GDE files.
 +
;[http://www.daimi.au.dk/%7Emailund/CoAnnealing/ CoAnnealing] : Simulated Annealing Search for Coalescent Trees.
 +
;[http://www.daimi.au.dk/%7Emailund/CoaSim/ CoaSim] : Simulating the coalescent process.
 +
;[http://www.daimi.au.dk/%7Ecompbio/comalign/index.html ComAlign] : Multiple alignment method that combine alignments toconstruct a good multiple alignment.
 +
;[http://birc.au.dk/Software/CombiBlock/ CombiBlock] : CombiBlock computes various versions of Hudson and Kaplans(1985) "minimum number of recombination event" statistics, R<sub>M</sub>, based on the Four-Gamete-Test. Further the programreturns a division of the data into blocks.
 +
;[http://birc.au.dk/old/Software/detector/index.html Detector] : Codon-based method for detecting changes in environmentspecific selection regimes.
 +
;[http://www.daimi.au.dk/%7Emailund/dprog/ DPROG] : A domain specific language for specifying dynamicprogramming algorithms; given a recursive definition of the problem,the compiler generates code for solving the problem using dynamicprogramming.
 +
;[http://www.daimi.au.dk/%7Emailund/drawtree.html Drawtree] : Drawtree is a program for visualisation of trees. It reads in trees in the Newick format and outputs them in a graphic format. Currently the only supported output format is Encapsulated PostScript, but other formats are planned.
 +
;[http://birc.au.dk/Software/EvoGene/ EvoGene] : Gene finding with a Hidden Markov Model of genomestructure and evolution.
 +
;[http://birc.au.dk/Software/GenePair/ GenePair] : The GenePair package implements a range of comparitive methodsfor gene structure prediction in homologous sequences.
 +
;[http://www.daimi.au.dk/%7Emailund/GeneRecon/ GeneRecon] : A coalescent based tool for fine-scale association mapping.
 +
;[http://www.daimi.au.dk/%7Emailund/HapCluster/index.html HapCluster++] : HapCluster++ is a software package for association mapping.
 +
;[http://www.daimi.au.dk/%7Ecstorm/hmmcomp/index.html HMMcomp] : Comparison of hidden Markov models.
 +
;[http://www.daimi.au.dk/%7Emailund/qdist.html QDist] : Computation of the quartet distance between evolutationary trees.
 +
;[http://www.daimi.au.dk/%7Emailund/quick-join.html QuickJoin] : A tool for fast neighbor-joining tree construction.
 +
;[http://birc.au.dk/Software/RBT/ RBT] : A tool for fast construction of refined Buneman trees,
 +
;[http://www.daimi.au.dk/%7Emailund/split-dist.html Split-dist] : Split-Dist calculates the number of splits (edges) that differs for two trees.
 +
;[http://www.daimi.au.dk/%7Emailund/suffix_tree.html SuffixTree] : The SuffixTree python module contains code wrapping a suffix tree implementation by Dotan Tsadoc and Shlomo Yona.
  
 
==Data acquisition (search engines)==
 
==Data acquisition (search engines)==
 +
*[http://www.visual-literacy.org/periodic_table/periodic_table.html A Periodic Table of Visualization Methods]
  
 
===Keyword===
 
===Keyword===
Line 64: Line 142:
 
*[http://www.sp2000.org/ Species 2000]
 
*[http://www.sp2000.org/ Species 2000]
 
*[http://www.ubio.org/ uBio] &mdash; uses names and taxonomic intelligence to manage information about organisms
 
*[http://www.ubio.org/ uBio] &mdash; uses names and taxonomic intelligence to manage information about organisms
 +
*[http://www.biolib.cz/en/main/ BioLib] &mdash; an international encyclopaedia of plants, fungi, and animals.
 +
*[http://www.forestryimages.org/ Forestry Images]
 +
*[http://www.iucnredlist.org/ The 2006 IUCN Red List of Threatened Species]
  
==Software==
+
==Software / Scripts==
 
*[http://www.biolinux.org/ BioLinux.org]
 
*[http://www.biolinux.org/ BioLinux.org]
 
*[http://rutchem.rutgers.edu/%7Exiangjun/3DNA/ 3DNA]
 
*[http://rutchem.rutgers.edu/%7Exiangjun/3DNA/ 3DNA]
 
*[http://skuld.bmsc.washington.edu/raster3d/raster3d.html Raster3D]
 
*[http://skuld.bmsc.washington.edu/raster3d/raster3d.html Raster3D]
 
*[http://emboss.sourceforge.net/apps/release/4.0/emboss/apps/ EMBOSS applications]
 
*[http://emboss.sourceforge.net/apps/release/4.0/emboss/apps/ EMBOSS applications]
 +
*[http://www.binf.ku.dk/~kasper/wiki/ScriptList.html Script List] &mdash; Bioinformatics related
  
 
==Other==
 
==Other==
Line 90: Line 172:
 
*[http://blaster.docking.org/zinc/ ZINC] &mdash; a free database of commercially-available compounds for virtual screening.
 
*[http://blaster.docking.org/zinc/ ZINC] &mdash; a free database of commercially-available compounds for virtual screening.
 
*[http://www.bio.sk/dir/ BIO.SK - Directory]
 
*[http://www.bio.sk/dir/ BIO.SK - Directory]
 +
;[http://birc.au.dk/old/Software/jambw/ jaMBW] : JaMBW, the Java based Molecular Biologist's Workbench.
 +
;[http://birc.au.dk/old/Software/SeWeR/ SeWeR] : SeWeR: Sequence Analysis using Web Resources is an integrated portal to commonly used bioinformatics tools on Internet and World Wide Web.
 +
;[http://birc.au.dk/old/Software/sms2/ SMS2] : The Sequence Manipulation Suite is a collection of JavaScript programs for generating, formatting, and analyzing short DNA and protein sequences.
  
 
==Wikis related to Bioinformatics==
 
==Wikis related to Bioinformatics==
 
*[http://wikiomics.org/wiki/Main_Page Wikiomics.org] &mdash; ([http://wikiomics.org/wiki/User:Christoph User:Christoph])
 
*[http://wikiomics.org/wiki/Main_Page Wikiomics.org] &mdash; ([http://wikiomics.org/wiki/User:Christoph User:Christoph])
 +
*[http://www.snpedia.com/index.php?title=SNPedia SNPedia]
 
*[http://omics.org/index.php/Main_Page Omics.org] &mdash; an openfree wiki site for -omes and -omics in Biotechnology and Bioscience.  
 
*[http://omics.org/index.php/Main_Page Omics.org] &mdash; an openfree wiki site for -omes and -omics in Biotechnology and Bioscience.  
 
*[http://openwetware.org/wiki/Main_Page OpenWetWare.org]
 
*[http://openwetware.org/wiki/Main_Page OpenWetWare.org]
 
*[http://rana.lbl.gov/drosophila/wiki/index.php/Main_Page AAA Wiki] &mdash; considers sequenced ''Drosophila'' genomes.
 
*[http://rana.lbl.gov/drosophila/wiki/index.php/Main_Page AAA Wiki] &mdash; considers sequenced ''Drosophila'' genomes.
 
*[http://biodomain.org/index.php/Main_Page openfree BioDomain.org] &mdash; a list of biological domains.
 
*[http://biodomain.org/index.php/Main_Page openfree BioDomain.org] &mdash; a list of biological domains.
 +
*[http://www.biodirectory.com/biowiki/Main_Page BioDirectory.com]
 +
*[http://www.mybio.net/biowiki/Main_Page MyBio.net]
 
*[[wikipedia:Bioinformatics]]
 
*[[wikipedia:Bioinformatics]]
 
*[[wikibooks:Computational Biology]] (aka Bioinformatics)
 
*[[wikibooks:Computational Biology]] (aka Bioinformatics)
 +
 +
==Lists==
 +
*[http://courses.washington.edu/bioinfo/BIR/ Biological Information Resource]
  
 
[[Category:Bioinformatics| ]]
 
[[Category:Bioinformatics| ]]

Latest revision as of 23:50, 20 June 2008

Source material

Bioinformatics related blogs

Databases

General

Genomes

Lists of genomes in progress

Genes / Proteins

Web servers

Catalytic Site Atlas (CSA) 
a database documenting enzyme active sites and catalytic residues in enzymes of 3D structure.
SiteEngine 
Functional Sites Structural Search Engine; Recognizes regions on the surface of one protein that resemble a specific binding site of another.
ASTRAL 
The ASTRAL Compendium for Sequence and Structure Analysis.
MolMovDB 
Database of Macromolecular Movements with Associated Tools for Flexibility and Geometric Analysis.
Dali Fold Classification 
based on exhaustive, all-against-all 3D structure comparison of protein structures in the Protein Data Bank
PDBsum 
provides an at-a-glance overview of every macromolecular structure deposited in the Protein Data Bank
BLOCKS 
a service for biological sequence analysis
Animators 
Visualization tools for the Wright-Fisher model and continous time coalescent.
CombAt 
Comparison of coding DNA that takes the encoded proteins into account.
distanceP 
Predict distance constraints between amino acids in proteins from the amino acid sequence.
FaBox 
FASTA online toolbox
FOLDALIGN 
Find the most significant common sequence and structure motifs in a set of RNA sequences.
GeMprospector 
Find cross-species genetic marker candidates online from a collection of plant ESTs.
Hudson 
Simulation of sequence evolution using the Hudson coalescent process to make a phylogony and the Jukes-Cantor substitution process.
MatrixPlot 
Generate mutual information plots of sequence alignments, distance matrices of sequence with known 3D coordinates, and plots of user provided matrix files.
Phy·fi 
Online tool for drawing Newick trees in color. Supports the JPG, GIF, PNG, TIF, PDF, and EPS formats.
PriFi 
Suggest primer pairs based on a DNA sequence alignment and give an account of the quality of the suggested primers.
RecPars 
Phylogenetic analysis using a parsimony analysis that takes recombination events into account.
Rateshift analysis 
Find signs of functional divergence as evidenced by shifts in evolutionary rates between two DNA, RNA or protein sub-families.
RetroSearch 
Database of ORF annotated human endogenous retroviruses.
RNA DB Tools 
Collection of tools which can be used to perform semi-automated update of RNA structural databases.
RNA Folding 
Find common secondary structures for multiple RNA sequences.
SLASH 
Stem-Loop Align SearcH. Search for a common stemloop motif in a relatively large data set.
StatAl 
Statistical alignment of DNA/protein sequences.
SRPDB 
Signal recognition particle database.
tmRDB 
tmRNA database ([1])

Downloadable Software

Blossoc 
Block-Association Mapping.
ClustalW Wrapper 
The clustalw python module contains code for wrapping the ClustalW multiple sequence alignment tool. Bundled with the ClustalW wrapper is also modules for reading FASTA and GDE files.
CoAnnealing 
Simulated Annealing Search for Coalescent Trees.
CoaSim 
Simulating the coalescent process.
ComAlign 
Multiple alignment method that combine alignments toconstruct a good multiple alignment.
CombiBlock 
CombiBlock computes various versions of Hudson and Kaplans(1985) "minimum number of recombination event" statistics, RM, based on the Four-Gamete-Test. Further the programreturns a division of the data into blocks.
Detector 
Codon-based method for detecting changes in environmentspecific selection regimes.
DPROG 
A domain specific language for specifying dynamicprogramming algorithms; given a recursive definition of the problem,the compiler generates code for solving the problem using dynamicprogramming.
Drawtree 
Drawtree is a program for visualisation of trees. It reads in trees in the Newick format and outputs them in a graphic format. Currently the only supported output format is Encapsulated PostScript, but other formats are planned.
EvoGene 
Gene finding with a Hidden Markov Model of genomestructure and evolution.
GenePair 
The GenePair package implements a range of comparitive methodsfor gene structure prediction in homologous sequences.
GeneRecon 
A coalescent based tool for fine-scale association mapping.
HapCluster++ 
HapCluster++ is a software package for association mapping.
HMMcomp 
Comparison of hidden Markov models.
QDist 
Computation of the quartet distance between evolutationary trees.
QuickJoin 
A tool for fast neighbor-joining tree construction.
RBT 
A tool for fast construction of refined Buneman trees,
Split-dist 
Split-Dist calculates the number of splits (edges) that differs for two trees.
SuffixTree 
The SuffixTree python module contains code wrapping a suffix tree implementation by Dotan Tsadoc and Shlomo Yona.

Data acquisition (search engines)

Keyword

Similarity

Multiple sequence alignment

Prediction

Phylogenetic analysis

Taxonomy

Software / Scripts

Other

jaMBW 
JaMBW, the Java based Molecular Biologist's Workbench.
SeWeR 
SeWeR: Sequence Analysis using Web Resources is an integrated portal to commonly used bioinformatics tools on Internet and World Wide Web.
SMS2 
The Sequence Manipulation Suite is a collection of JavaScript programs for generating, formatting, and analyzing short DNA and protein sequences.

Wikis related to Bioinformatics

Lists