Difference between revisions of "Bioinformatics links"

Latest revision as of 23:50, 20 June 2008

• Bioinformatics Links Directory

Source material

• PubMed
  • Hardcore PubMeding (advanced PubMed searching)
• HubMed
• PubMed Reader
• Authoratory

Bioinformatics related blogs

• Computational Biology - Bioinformatics Blogs — long list of blogs
• PostGenomic
• Notes from the Biomass
• Flags and Lollipops
• Bio::Blogs
• BioHacking
• Systems Biology & Bioinformatics
• RNA Bioinformatics
• LabAction — Human Genetics,Science Projects,Science Experiments
• Fungal Genomes and Comparative Genomics
• The Tree of Life — blog of Jonathan A. Eisen
• note2self
• BMI Students
• Flags and Lollipops
• Eye on DNA

Databases

• wikipedia:Biological_database

General

• European Bioinformatics Institute — portal for research and services in bioinformatics, with databases of nucleic acid and protein sequences, and macromolecular structures - from the EMBL, Hinxton UK.
• NCBI/GenBank (USA) — offers many important databases (PubMed, GenBank, OMIM) and some tools.
• DDBJ (Japan)
• CrossRef

Genomes

• TIGR
• JGI
• Sanger
• NCBI
• UCSC ENCODE Project (includes latest, most complete build of the Human genome)

Lists of genomes in progress

• Genome projects
• http://wit.integratedgenomics.com/GOLD/
• http://www.tigr.org/tdb/mdb/mdbinprogress.html
• Ensembl genome download (mainly Eukaryotes)
• Complete Published Genome Projects: 524

Genes / Proteins

• [http://www.ncbi.nlm.nih.gov/sites/entrez?db=OMIM Online Mendelian Inheritance in Man (OMIM)
• PPID - Protein to Protein Interaction Database
• Bioinformatic Harvester III (beta)
• iHOP - Information Hyperlinked over Proteins

Web servers

• World Index of BioMolecular Visualization Resources
• PDBSiteScan
• SuMo
• SCOP: Structural Classification of Proteins
• Vienna RNA Secondary Structure Prediction
• Searching for 3D functional sites in a protein structure
• wikipedia:Structural genomics
• Bioinformatic Harvester III (beta)

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, R_M, 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)

• A Periodic Table of Visualization Methods

Keyword

• SRS (tutorials can be found at http://www.icgeb.trieste.it/~netsrv/courses/RH/srs/ or http://www.no.embnet.org/Programs/DB/srs_tut.php3)
• Entrez (tutorial can be fond at http://www.ncbi.nlm.nih.gov:80/Database/tut1.html)

Similarity

• BLAST

Multiple sequence alignment

• ClustalX (ftp) (tutorial can be found at http://www.bioinf.org/molsys/ClustalX_tutorial.html)
• BioEdit
• BCM search launcher
• GCG
• Lists
• STRAP — Multiple Sequence Alignment

Prediction

• NNPREDICT — Protein Secondary Structure Prediction
• Pattern and profile searches Pattern and profile searches

Phylogenetic analysis

• PAUPp (tutorial can be found at http://paup.csit.fsu.edu/Quick_start_v1.pdf)
• Mega2
• PHYLIP
• Treeview
• List

Taxonomy

• Species 2000
• uBio — uses names and taxonomic intelligence to manage information about organisms
• BioLib — an international encyclopaedia of plants, fungi, and animals.
• Forestry Images
• The 2006 IUCN Red List of Threatened Species

Software / Scripts

• BioLinux.org
• 3DNA
• Raster3D
• EMBOSS applications
• Script List — Bioinformatics related

Other

• Bioinform — bioinformatics news service.
• Bioinformatics.ca — curated web directory of molecular biology and bioinformatics resources
• Bioinformatik — categorical web directory for bioinformatics theory - from the Univ. of Düsseldorf. Mathematics and Computer-based.
• Bioplanet Jobs — bioinformatics jobs, education resources, bulletin board, CV posting.
• Canadian Bioinformatics Resource — dedicated to providing researchers with convenient, effective access to high-quality bioinformatics tools and databases.
• CMS Molecular Biology Resources — a compendium of tools for molecular biology, biotechnology, molecular evolution, biochemistry and biomolecular modeling.
• DNA and Protein Analysis Toolkit — compendium of bioinformatics computing services from The Rockefeller University. Many different ways to analyse biomolecules.
• Genome Programs — links to online genomics resources - including the individual projects.
• Molecular Biological Sites — includes sequence search windows, as well as databases and tools related with proteomics and structural bioscience.
• Snowdeal.org — a weblog that provides daily updates and links to news items and stories of interest to bioinformatics community.
• UBC Bioinformatics Centre Resource Directory — currated and categorized database of links to the top bioinformatics and molecular biology resources on the web.
• The OpenScience Project
• Quick guide to characteristics of metal sites in proteins
• sfcheck — a program for assessing the agreement between the atomic model and X-ray data or EM map.
• OmicsWorld
• OMICS: A Journal of Integrative Biology
• ZINC — a free database of commercially-available compounds for virtual screening.
• BIO.SK - Directory

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

• Wikiomics.org — (User:Christoph)
• SNPedia
• Omics.org — an openfree wiki site for -omes and -omics in Biotechnology and Bioscience.
• OpenWetWare.org
• AAA Wiki — considers sequenced Drosophila genomes.
• openfree BioDomain.org — a list of biological domains.
• BioDirectory.com
• MyBio.net
• wikipedia:Bioinformatics
• wikibooks:Computational Biology (aka Bioinformatics)

Lists

• Biological Information Resource