Prediction of disordered regions

DisEMBL

GlobPlot

MeDor

POODLE

Sequence aligment

Binary

LALIGN

Dotlet

Multiple

Decrease redundancy

CLUSTALW

KALIGN

MAFFT

Muscle

T-Coffee

MSA

DIALIGN

Match-Box

Multalin

MUSCA

Alignment Analysis

AMAS

Bork's alignment tools

CINEMA

ESPript

MaxAlign

PhyloGibbs

SVA

PVS

WebLogo

plogo

GENIO/logo

SeqLogo

Phylogenetic Analysis

BIONJ

DendroUPGMA

PHYLIP

PhyML

Phylogeny.fr

The PhylOgenetic Web Repeater (POWER)

BlastO

Evolutionary Trace Server (TraceSuite II)

Phylogenetic programs

Biological Text Analysis

AcroMed

BioMinT

GPSDB

Medline Ranker

The Miner Suite

XplorMed

Statistical tools

pROC

Nucleic Acid Analysis

Calculators/Unitilies

4PEAKS

BIOCALCULATORS (AGILENT)

BIOMATH CALCULATORS

DNA 2.0 BIOINFORMATICS TOOLBOX

GenoCAD

iPapers

LabAssistant 1.1

MARTINDALE’S BIOSCIENCE CALCULATORS ON-LINE CENTER

PAPERS

READSEQ SEQUENCE CONVERSION (EBI)

REVERSE COMPLEMENTING A DNA SEQUENCE

THE GENETIC CODES

TRANSEQ

TRANSLATE TOOL

UNIVERSAL GENETIC CODE

VIRTUAL RIBOSOME

ANNO-J

Exons and alternative Splicing

AGenDA: ALIGNMENT-BASED GENE DETECTION ALGORITHM

ALTERNATIVE EXON DATABASE (EBI)

ALTERNATIVE SPLICING AND TRANSCRIPT DIVERSITY

ALTEXTRON (EBI)

ALTSPLICE (EBI)

ATDB: ALTERNATIVE TRANSCRIPT DIVERSITY DATABASE (EBI)

AUGUSTUS

CODON USAGE DATABASE

CPGPLOT

DEDB: DROSOPHILA MELANOGASTER EXON DATABASE

EASYGENE

ESEfinder: EXONIC SPLICING ENHANCER FINDER (CSHL)

EuGENE’HOM

EXON PAINTER

FeatureExtact

FrameD

FUGOID: FUNCTIONAL GENOMICS OF ORGANELLAR INTRONS DATABASE

GeneFizz

GeneMark

GENIE: GENE FINDER 

GENSCAN (MIT)

GLIMMER: MICROBIAL GENE-FINDING SYSTEM

H-DBAS: HUMAN-TRANSCRIPTOME DATABASE OF ALTERNATIVE SPLICING

HMMGENE

HS3D: HOMO SAPIENS SPLICE SITES DATASET

JCAT: JAVA CODON ADAPTATION TOOL

mGene.web

NETGENE2

NetPlantGene

ORF FINDER (NCBI)

ORPHELIA

ProSAS: PROTEIN STRUCTURE AND ALTERNATIVE SPLICING DATABASE

RESCUE-ESE: EXONIC SPLICING ENHANCERS

SERpredict

SHORT TANDEM REPEAT DNA DATABASE

SLAM: WHOLE GENOME ANNOTATION OF HUMAN AND MOUSE

SPLICEINFO

SpliceNest

SROOGLE: SPLICING REGULATION ONLINE GRAPHICAL ENGINE

TACT: TRANSCRIPTOME AUTO-ANNOTATION CONDUCTING TOOL

TACT: TRANSCRIPTOME AUTO-ANNOTATION CONDUCTING TOOL

THE GENETIC CODES

VIRTUAL RIBOSOME

WASP: WEBSITE FOR ALTERNATIVE SPLICING PREDICTION

Expressed sequence tags

dbEST: EXPRESSED SEQUENCE TAGS DATABASE

ECGENE: EST CLUSTERING

EDAS: EST-DERIVED ALTERNATIVE SPLICING DATABASE

MGALIGN: mRNA TO GENOME ALIGNMENTS

MIRA 2 EST SEQUENCE ASSEMBLER

UNIGENE

WEBGESTALT: WEB-BASED GENE SET ANALYSIS TOOLKIT

Literature Gateaway

BIOMED CENTRAL: OPEN ACCESS

BioMinT

ENTREZ (NCBI)

etBLAST

GOOGLE SCHOLAR

GOPUBMED

HUBMED: PUBMED REWIRED

IHOP: INFORMATION HYPERLINKED OVER PROTEINS

LitInspector (Genomatix)

LITMINER

MedlineRanker

NCBI EMAIL ALERTS

NLM GATEWAY

OLS: ONTOLOGY LOOKUP SERVICE

PLOS: PUBLIC LIBRARY OF SCIENCE

PUBCRAWLER

PUBGENE

PUBMATRIX

PUBMED

PUBMED CENTRAL

SCIRUS

SENT: SEMANTIC FEATURES IN TEXT

SEQANALREF (EXPASY)

Mirna Sequences and Targets

ASRP: Arabidopsis thaliana SMALL RNA PROJECT

CROSSLINK

DIANA-microT

deepBase

GeneSet2miRNA

INSERT DESIGN TOOL (AMBION)

MICROCOSM

MicroInspector

microRNA TARGETS

miPRED

miRacle

MiRAlign

miRanalyzer

miRBASE REGISTRY (SANGER)

miRBASE SEQUENCE DATABASE (SANGER)

mirDEEP

MiRNA TARGET SEARCH

miRNAMap

miRpredict

MirZ

MMIA: microRNA AND mRNA INTEGRATED ANALYSIS

ProMiR II

psRNATARGET

RegRNA: REGULATORY RNA MOTIFS AND ELEMENTS FINDER

RNA22 MICRORNA TARGET DETECTION (IBM)

RNAhybrid

smiRNAdb

TARGETSCAN

TargetScanS

TransmiR

ViTa: VIRUS miRNA TARGET

Molecular Biology Protocols

BENCH GUIDE (QIAGEN)

BIOTECHNIQUES® PROTOCOL GUIDE 

BIOWWW.NET

COLD SPRING HARBOR PROTOCOLS

JOVE: JOURNAL OF VISUALIZED EXPERIMENTS

LINNEA™ PROTOCOLS

NUCLEIC ACIDS RESEARCH METHODS

Nucleic Acids Structure

3D-DART: 3DNA-DRIVEN DNA ANALYSIS AND REBUILDING TOOL

3D-FOOTPRINT

3DNALandscapes

4SALE: RNA SEQUENCE ALIGNMENT AND EDITING

bend.it® SERVER

CENTROIDFOLD

dbRES: DATABASE FOR RNA EDITING SITES

DIAL: DIHEDRAL ALIGNMENT SERVER

DINAMELT SERVER

DNA mFOLD

DNA TOOLs

FASTR3D: FAST AND ACCURATE SEARCH TOOL FOR RNA 3D STRUCTURES

NDB GALLERIES

NDB: NUCLEIC ACID DATABASE

ProNIT: PROTEIN-NUCLEIC ACID INTERACTIONS

PROTEIN-RNA INTERACTION DATABASE

RNA mFOLD

RNA MODIFICATION DATABASE

RNA NON-CANONICAL PAIR DATABASE

RNAmine

RNAVIZ

SARA

SSTRUCTVIEW

TINOCO PLOT

w3DNA

WEB 3DNA

Primer Design

ARRAY DESIGNER

ASePCR: ALTERNATIVE SPLICING ELECTRONIC RT-PCR IN MULTIPLE TISSUES

ASSEMBLY PCR OLIGO MAKER

AUTODIMER

CODEHOP: CONSENSUS DEGENERATE HYBRID OLIGONUCLEOTIDE PRIMERS

D-LUX™ DESIGNER (INVITROGEN)

DILUTIONCALCULATOR (IDT)

DNA METHYLATION ANALYSIS PCR PRIMER DATABASE

e-PCR: ELECTRONIC PCR

GENE DESIGNER

GENE2OLIGO 

GENEFISHER

geNorm

iCODEHOP: CONSENSUS DEGENERATE HYBRID OLIGONUCLEOTIDE PRIMERS 

IDT SCITOOLS (IDT)

IN-SILICO PCR

iRNAi

LNA TOOLS

methBLAST

MethPrimer: METHYLATION PCR

MULTIPLEX MANAGER

muPLEX: MULTI-OBJECTIVE MULTIPLEX PCR DESIGN

NormFinder

OLIGOANALYZER (IDT)

OLIGODESIGN

OligoPerfect™ DESIGNER (INVITROGEN)

PCR SUITE

PDA: PRIMER DESIGN ASSISTANT

PRIMACLADE

PRIMEGENS: PRIMER DESIGN USING GENE SPECIFIC FRAGMENTS

PRIMER -BLAST (NCBI)

PRIMER BANK

PRIMER DESIGN FOR AUTOMATED SEQUENCING

PRIMER Z

Primer3Plus

PRIMERQUEST (IDT)

primers4clades

PRIMERSTATION

PRIMERX

probeBase: rRNA-TARGETED OLIGONUCLEOTIDE PROBES

PROBEWIZ

qPimerDepot: QUANTITATIVE REAL-TIME PCR PRIMER DATABASE

QPPD: QUANTITATIVE PCR PRIMER DATABASE

qPrimerDepot: QUANTITATIVE REAL TIME PCR (HUMAN)

qPrimerDepot: QUANTITATIVE REAL TIME PCR (MOUSE)

RESUSPENSION CALCULATOR (IDT)

RTPrimerDB: REAL TIME PCR PRIMER AND PROBE DATABASE

SCPrimer

SNPbox

SNPDesign 

TmPrime

Uniprime: UNIVERSAL PRIMER DESIGN

UniSTS

VirOligo

WEB PRIMER (SGD)

Restriction site Mapping

ApE PLASMID EDITOR

DOUBLE DIGEST FINDER

ENZYME FINDER (NEB)

EnzymeX

everyVECTOR

GeneCoder

NEB CUTTER

REBASE® (NEB)

RESTRICTION ENZYMES AND METHYLASES

Vector NTI ADVANCE® (Invitrogen)

WEBCUTTER