THOSE ARE MY SCIENCE LINKS

The picture is a clickable map!

USEFUL LINUX/UNIX INFORMATION
Gentoo-Linux
TLPD	The Linux Documentation Project
LUCAS	LINUX Documentation project in Spanish
UNIX	Reference Desk
Unix	mini-HowTo
Commands	Commonly used Unix commands
Safari	Beginning Perl for Bioinformatics
BioPerl	A MUST! FOR BIOLOGISTS!
PERL	A PERL MANUAL
MySQL	A MANUAL
HTLM	THE GUIDE! super-cool
C++	manual

Bioinformatic places
KEGG	Kyoto Encyclopedia of Genes and Genomes
EBI	European Bioinformatics Institute
NCBI HomePage	BLAST, PubMed, and associated tools
Go there	Bioinformatics Links
PASTEUR	The Institute Pasteur Site
The Bio-Web	DNA and Protein Sequence Analysis Tools
Dr. Matrix Biology	A Very interesting place
BioExchange.com Tools	Genomics and Bioinformatics Tools, Biology Resources, Protocols
The Web Sites	A virtual library

USEFUL SOFTWARE
FOR SEQUENCE ANALYSES AND MULTIPLE ALIGNMENT
T-COFFEE	For multiple alignments
Indonesia Manual	Biological sequence analyses
W2H Welcome	Sequence analyses
Web Resources	Molecular Evolution and Systematics
Welcome to the Huelsenbeck Lab!	Evolutionary biology
Web Resources	Molecular Evolution and Systematics
Welcome to the Huelsenbeck Lab!	Evolutionary biology
ForCon	Multiple alignment conversion tool
MEGA2	Evolutionary analysis software
WU-Blast2 blast	A different version of BLAST 2 sequences
Alternatives to GCG	This is a MUST!!!
EST_genome	A program to align a spliced DNA sequence to an unspliced genomic sequence
FORESTER	Phylogenomics
FOR Gene prediction
Gene Finding	Gene prediction
GeneMachine	Comparative and predictive gene identification techniques
FOR clustering and graph drawing
Graphviz	COOL tool FOR DRAWING GRAPHS
CLUTO	clustering: HIGH Dimensional DATASETSCLUSTERING package
For Molecular Graphics
Protein Explorer	Visualization tool: A Tutorial
RasMol	Visualization tool: homepage
BobScript
CONSCRIPT	a programm for generating electron density isosurfaces
ENDscript
ESPrip
GRASP
MolMol
Molscript
MolSof
Povscript+
Pov4Grasp	A patch version of POV-ray with direct support for GRASP surfaces
QUE
Rarter3D
Spock
Strucutural	sOME STRUCTURAL AND xTALL PROGRAMS!
SOFTWARE SITES
ISREC GROUP	The ISREC Software Homepage
TIGR	Software Tools - The Institute for Genomic Research
Barton's group Software
DNA: transcription	Software for the analysis of DNA sequence elements of transcription
MDscan	Chromatin Inmuno precipitation
Strucutural	sOME STRUCTURAL AND xTALL PROGRAMS!
Production software for Biologists	WIDE SPECTRUM
NHGRI	DIR Research Projects
http://rulai.cshl.edu/")	Software for genomics
MZEF	Documentation
EMP Project
BIMAS project	Supported Molecular Biology Software
Biological software
Software links
Bioinformatics Software on the Web

GENOMICS RELATED
Genomics	123 Genomics - Sequence analysis, data mining, gene hunting, genomic mining, protein analysis, structure prediction
Gene prediction	GenomeScan Promoter 2.0 Server GENE PREDICTIONS on GENOMES
Exon finders	BDGP Neural Network Promoter Prediction: Input operons predictor Web Signal Scan Service Zhang lab GrailEXP Home Page Genomatix. Requires registration but cool! FunSite GeneMark Help File TFBINDING SITES FINDER: INPUT TFSEARCH: find Transcription Factors!! Promoter Recognition (FunSiteP) 2.1 About PROGRAM TO RECOGNIZE EUKARYOTIC PROMOTERS Integrated System for Michael Zhang's MZEF and Thanaraj's SpliceProximalCheck GrailEXP Frequently Asked Questions (FAQ) v1.2 BDGP: Neural Network Promoter Prediction: Input Promoter 2.0 Server McPromoter promoter prediction server Procrustes NOTE: Phased out!Gene Recognition via Spliced Alignment New GENSCAN Web Server at MIT [Bioperl-l] Bio::Tools::MZEF ORF Finder Ensembl Zebrafish Genome Server Ensembl Genome Browser BLAT Search UCSC GENOME (GOOD) binding sites analysis EPCLUST: data clustering and analysis The Sanger Institute : Danio Rerio Sequencing Project Interactive Genie SYNTENIC GENE PREDICITION

ORGANISMS
GENOME SIZES	Some statistics
SHEEP	UK sheep genome mapping project
Fugu	JGI
Zebrafish	Genome Resources Project
ZFIN Catch of the Day	MORE ZEBRAFISH
CIONA	DOE Ciona intestinalis-Ascidian SITE
CHICKEN	CHICK EST's collection

BLAST SEARCHES
Entrez-Protein	Proteins
ALL the BLAST SERVERS!!!!	Blasting...
NCBI BLAST Home Page
CMR BLAST	TIGER
Zebrafish	Blast Search
JGI	Ciona BLAST Search
Zon Lab	Blast Sequence Retrieve

MASKING DNA
RepeatMasker	Web Server
ZBF	Repeat Masker For zebrafish

GENERAL STUFF: CUTTING AND PRIMERS

General Stuff

DNALC	A Biology Animation Library
Aminaocids	Physical Classification of Amino Acids

Primer Design

PCR	Primer Design theory
More..	Primer Design Programs
PCRaplt	Primer Design Program
GENEFISHER	Interactive primer design (Very Good)
Web Primer	DNA and Purpose Entry
Primer design (Rockefeller)

Cutting DNA

Webcutter 2.0
WWWtacg Ver 2.38 Form
Restriction Enzyme Analysis tools	cool

SELECTED DATABASES
PROTEIN DATABASES
SCOP	Structural Classification of proteins
PDB	Protein Data Bank: the repository
CATH	Protein Structure Calssification
INTERPRO	Domain Database
BRENDA	Functional Database
FSSP	Structural: DALI fold classification OUT-PHASED!
DALI-interactive	Structural Neighbours
PQS-EBI	Protein Quaternary Structure Database
NUCLEAR LOCALIZATION SIGNAL
PredictNLS Online	Nuclear Localization Signal
PredictNLS	Prediction and Analysis of NLSs
NLSdb	Server
OTHER STUFF
MEROPS database	The Proteases Database
FUGU	FUGU sequences for FTP

Databases LINKS

Databank Information

Entigen \| Databanks

TIGR Microbial Database
GENOMIC NAVIGATORS, ETC
ASDB	Alternative Splicing DB (ASDB) - Main Page
SeqTools	Gene/Sequence Resources
EUKA	PROMOTER DATABASE
IMGT/HLA	Database
Genome Databases	More Databases Genomic resources
Webminer	MEGADATABASE about yeast exp
Genome Channel Organism Navigation	More Genome Resources
Other Genomic Databases	Other Genome Resources
ARKdb	Public Database Borwser
EUKintronDB	Eukarya, introns
HGMP-RC	Fugu Genomics Project
Genetic Databases	More Databases
BASED ON TRANSCRIPTION FACTORS
TRANSFAC	Guided Tour
TRANSFAC	Classification of Transcription Factors
TESS	Database of Transcription Factors
BASED ON INTERACTIONS
DIP	HOME
DNA-Protein Binding	Home Page
BIND	The Biomolecular Interaction Network Database

GENERAL SEQUENCE ANALYSES
Resources	Sequence Analysis on the Web
CODOB	Codon Usage Tables
RACC	RARE CODON CALCULATOR
READSEQ	Format Sequence Conversion tool
fmtseq	BioSeq File Format Conversion
Translator
BCM-SEARCH LAUNCHER!	Welcome to the BCM Search Launcher
Clustering Calculator
RESMAP	Restriction Mapping

PATTERN RECOGNITION

Gibbs Sampling

Repetitive element prediction

Block Maker

Ballast

The Gibbs Motif Sampler Homepage

ALIGNMENTS
ALIGNMENT EDITORS
BOXSHADE (Web based)
GENEDOC alignment editor (Windows)
BELVU (Linux)
JalView (Linux)
Sequences Alignments and Comparisons
STRUCTURES
MAPS: Mulitple Alignment of Protein Structures
CE Combinatorial Extension
STRUCLA: phylogeny
CONSURF
SEQUENCES
HMMER in a server!
SAM-T99 Alignment Tuneup
T-Coffee: A Consistency Based Multiple Alignmnent Method Multiple Alignments
UCSC HMM Applications Main Page
GENOMIC ALIGNMENTS
Vista Home
MUMer plot and Gene Display (WHOLE GENOMES)
SIM4 - a program to align cDNA and genomic DNA
PipMaker Instructions
PipMaker and MultiPipMaker

PHYLOGENIES AND EVOLUTION

Genetic and Phylogenetic Analysis

phylogenetic resources

Phylodendron - Phylogenetic tree printer

TREE BUILDING

Phylip

Phylogeny : Phylip programs

PHYLIP (Phylogeny Inference Package): Introduction

PHYLIP protein programs

Other stuff

Molecular Evolutionary Genetics Analysis MEGA

TreeTop - Phylogenetic Tree prediction

GeneTree

cDNA

SNAP: SvsNS substitutions

SNAP Info page

PROT PREDICITION SERVERS

PROTEIN STRUCTURE PREDICTION CENTER

Go to Osvaldo's Page: comprehensive list of all the protein prediction stuff

PROTEINS

Topology Cartoons

Jpred - A consensus secondary structure prediction server

OLDERADO best nmr MODEL

Bayesian Bioinformatics at Wadsworth Center

Xtallography links

ExPASy - Tools

The ConSurf Server

Protein Multiple Sequence Analysis

ExPASy - ProtParam tool

MOTIFS AND DOMAINS

I-Sites library

INTERPRO

PFAM

PREDICTIONS AND STRUCTURAL SEARCHES

PDG. CNB-CSIC. Contact Prediction Server

EMBL Dali: email server for 3-D protein structure database searches

Xtallography links

EMBL Dali: email server for 3-D protein structure database searches

Protein structure similarity searching in SCOP database

Meta PP introduction

Coiled Coils

COILS Server

Multicoil Scoring Form

PredictProtein: structure prediction and sequence analysis

FOLDING

ROBETTA (ab-initio)

HMMSTR/ROSETTA Server

BIOINFORMATIC SERVES AT THE BURNHAM

FFAS+: new search

LIBELLULA

Genesilico metaserver

DOMAIN ARCHITECTURE

SMART - Simple Modular Architecture Research Tool

STRING - Interacting genes proteins

CRYSTALLOGRAPHY / STRUCTURE ANALYSIS LINKS (COURTESY OF MY FRIEND JOSE)

Structure Solution

Molecular Replacement

Heavy atoms:

Model building

Molecular Graphics

BobScript
CONSCRIPT: a programm for generating electron density isosurfaces
ENDscript
ESPrip
GRASP
MolMol
Molscript
MolSof
Povscript+ :
Pov4Grasp : a patch version of POV-ray with direct support for GRASP surfaces
QUE
Rarter3D
Spock

Struture analysis

CaPTURE, cation-pi interaction analysis
castP: A Server for Identification of Protein Pockets & Cavities
ConSurf server: identification of functional regions in proteins
DALI
Evolutionary Trace Server
Indonesia : integrated program package for biological sequence analysis. Includes Structure-based multiple sequence alignment.
LigPlot : schematic diagrams of protein-ligand interactions.
MolProbity
PARVATI : Protein Anisotropic Refinement Validation and Analysis
PINTS: Patterns in Non-homologous Tertiary Structure
PRODRG Server-Dundee
Protein-Protein Interaction Server
SSBOND : Model building of disulfide bonds (Bart Hazes)
Stralign: Structure alignment for 3D protein structures.
SURFNET : Surfaces, cavities, etc.
TOPS : protein topology cartoons (EBI)
Uppsala Software Factory (USF).