Primer3Plus Pick primers from a DNA sequence.
DimerChecker Check the possible primer dimers and hairpins
AutoDimer Rapidly screen PCR primers for primer-dimer and hairpin interactions.
#################################
Secondary structure folding:
RNAfold web server Predict secondary structures of single stranded RNA or DNA sequences.
RNAstructure For RNA and DNA secondary structure prediction and analysis.
RNAsoft Software for RNA/DNA secondary structure prediction and design
#################################
Multiple Sequence Alignment:
CLUSTALW Multiple Sequence Alignment tools
#################################
Motif search
TFSEARCH Searching Transcription Factor Binding Sites (ver 1.3)
Dimont A universal tool for de-novo motif discovery
RestrictionMapper On line restriction mapping the easy way.
ORF Finder Open Reading Frame Finder
#################################
siRNA design:
RFRCDB-siRNA Design of siRNA with Random Forest Regression Model Coupled with Database Searching
OligoWalk An online siRNA design tool utilizing hybridization thermodynamics
siDRM An effective and generally applicable online siRNA design tool
siRecords An extensive database of mammalian siRNAs with efficacy ratings
DSIR Designer of Small Interfering RNA
RNAiAtlas A database for RNAi (siRNA) libraries and their specificity.
E-RNAi A web application for the multi-species design of RNAi reagents
OptiRNA For ranking siRNA target sites
OptiRNAi An RNAi Design Tool
siVirus Website for efficient antiviral siRNA design.
Sfold For statistical folding and rational design of nucleic acids.
TROD T7 RNAi Oligo Designer.
Deqor v3 A web-based tool for the design and quality control of siRNAs.
#################################
miRNA:
miRBase MicroRNA database.
ChIPBase Decoding transcription factor binding maps and transcriptional regulation.
Tarbase Capturing the Exponential Growth of miRNA Targets with Experimental Support.
miRecords A resource for animal miRNA-target interactions.
PicTar An algorithm for the identification of microRNA targets.
PITA Predicted microRNA targets.
RNA22 MicroRNA target detection.
MicroCosm Predicted microRNA targets.
MiRNAMap Genomic maps of microRNAs in metazoan genomes
For Plant
miRU,psRNATarget A plant small RNA target analysis server
Target-align A tool for plant microRNA target identification
#################################
Deep sequence analysis:
miRDeep2 Discovering known and novel miRNAs from deep sequencing data
miRDeep* An integrated application tool for miRNA identification from RNA sequencing data.
deepBase Deeply exploit the deep sequencing data
miRDeepFinder An comprehensive workflow of analyzing data from plant miRNA deep sequencing
mirTools2.0 For non-coding RNA discovery, profiling and functional annotation
miRspring A compact standalone research tool for analyzing miRNA-seq data.
#################################
Sequence Mapping Tool
Bowtie Ultrafast short read alignment
Bowtie2 Fast and sensitive read alignment
BWA Software for mapping low-divergent sequences against a large reference genome
SeqMap Short Sequence Mapping Tool
HSA A Heuristic Splice Alignment Tool
Tophat RNA-Seq splice junction mapper
Cufflinks Isoform assembly, quantitation
IGV High-performance genomics data visualization and exploration
SAMtools Provide various utilities for manipulating alignments in the SAM format
#################################
miRNA primer design:
miRNA primer designer For stem-loop RT-PCR
miRprimer A tool for design of primers for microRNA-specific quantitative RT-qPCR.
miRNA primer design tool For stem-loop RT-PCR
#################################
piRNA:
piRNABank A web resource on classified and clustered piRNAs
piRNA cluster Database
proTRAC Detects genomic piRNA clusters based on NGS datasets
piRNApredictor A software for predicting piRNA sequences.
#################################
CRISPR sgRNA:
没有评论 :
发表评论