mirTools 2.0 - for non-coding RNA discovery, profiling and functional annotation based on high-throughput sequencing
for non-coding RNA discovery, profiling and functional annotation based on high-throughput sequencing
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Reanalyze - Exome assistant - Rapid and easy detection of disease-related genes and genetic variations from exome sequencing
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Single case
Two cases
Group cases
Re-analysis
Re-analysze
Users can use this facility to re-analyze previous submitted samples. You can assign the job ID and set the parameters . Then, mirTools 2.0 will re-analyze your data to avoid of submitting the samples once again.
Please put you jobID in following box
ID number:
*
Sequences parameters
Reference genome selection
Reference Genome:
Human(hg19)
Chimpanzee(panTro2)
Gorilla(gorGor3.1)
Orangutan(ponAbe2)
Gibbon(Nleu1.0)
Rhesus(rheMac2)
Horse(equCab2)
Mouse(mm10)
Rat(rn4)
Cow(bosTau4)
Dog(canFam2)
Chicken(galGal3)
Zebrafish(Zv8)
Pig(susScr3)
Platypus(OANA5)
Opossum(monDom5)
Xenopus tropicalis(xenTro3)
Arabidopsis thaliana(TAIR10)
Zea mays(AGPv2)
Vitis vinifera(IGGP_12x)
Populus trichocarpa(JGI2.0)
Oryza sativa(MSU6)
Glycine max(V1.0)
Sorghum bicolor(Sorbi1)
Anolis carolinensis(anoCar2)
Ciona intestinalis(ci2)
Caenorhabditis elegans(ce10)
Drosophila melanogaster(BDGP5)
Apis mellifera(Amel_2.0)
Anopheles gambiae(anoGam1)
Sarcophilus harrisii(DEVIL7)
purple sea urchin(strPur2)
Length of interval:
16
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20
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25
26
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28
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31
32
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Your email
:
(Optional)
ncRNA annotation and profiling
Parameters for SOAP to align reference genome:
M value:
0
1
2
4
Match mode: 0=exact; 1=1 mismatch; 2=2 mismatch; 3=all; 4=the best
R value:
0
1
2
How to report repeat hits: 0=none; 1=random one; 2=all
V value:
0
1
2
3
4
Maximum number of mismatches
Parameters for MEGABLAST to align miRBase and Rfam:
E value:
1
0.1
0.01
0.001
0.0001
Expect value
B value:
1
2
3
4
5
Number of database sequence to show alignments for (B)
V value:
1
2
3
4
5
Number of database sequences to show one-line descriptions for (V)
Filter for miRNA isoform:
Absolute reads count >:
Contributes to the total number (%):
Use Z-score cut-off :
Novel miRNA prediction
miReap
miRDeep
Parameters for novel microRNAs prediction tools
miReap
L value:
Flank sequence length of the query. Range 0 - 200
miRDeep
V value:
The score cut-off which reflects the probability that the hairpin is a genuine miRNA precursor
miRNA targets prediction and functional annotation
Parameters for miRNA targets prediction:
Select the top abundant miRNA for targets prediction
Known miRNA:
10
20
30
Novel miRNA:
10
20
30
Select main tools for targets prediction
miRanda
RNAhybrid
Parameters for miRNA targets prediction tools
miRanda
Energy: Minimal free energy (MFE)
Score:
RNAhybrid
Energy: Minimal free energy (MFE)
P value:
Select additional tools for miRNA for targets prediction.
MicroCosm
microT_v3.0
MirTarget2
miRNAMap
TargetScan
TargetSpy
Parameters for GO and Pathway analysis of miRNA targets:
Parameters for GO analysis
P value: The threshold for hypergeometric test
Enrichment fold:
Parameters for Pathway analysis
P value: The threshold for hypergeometric test
Enrichment fold:
Parameter for protein-protein interaction analysis of miRNA targets:
Score:
Differential expression analysis
Parameters for detection differentially expressed ncRNAs
P value:
0.05
0.01
0.005
op
0.001
P value inferred based on Bayesian method
D value:
1
1.5
2
2.5
3
3.5
4
Fold change in normalized sequence counts
Filter SNPs
Annotation:
dbSNP
Novel
None
Known or novel SNPs in comparison with dbSNP
HapMap:
CEU
YRI
CHB
JPT
SNPs corresponding to HapMap project
Mutation Type:
Homozygous
Heterozygous
None
SNPs of Homozygous or heterozygous
SNPs classification:
Missense
Nonsense
Splice site
Readthrough
Synonymous-coding
5'UTR
3'UTR
Intergenic
Intron
SNPs classification based on the impact of potein
Impact of protein function:
Damage
Tolerated
None
Functional impact of SNPs
Filter InDels
Annotation:
dbSNP
Novel
None
Known or novel InDels in comparison with dbSNP
Range of genome:
Coding
Noncoding
None
The distribution of InDel sites
Mutation Type:
Homozygous
Heterozygous
None
InDels of homozygous or heterozygous
Amino Acid Change:
AA-Insertion
AA-Deletion
Frameshift
Institute of Genomic Medicine, Wenzhou Medical College
Wenzhou 325035, Zhejiang, China