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  BLAST
- BLAST Tutorial
- About using tools
Query: Enter FASTA sequence
Alignment Options
General Parameters
Program:
Max target sequences:
E-value:  
Word size:  
Max matches in a query range:  
Scoring Parameters
Match/Mismatch Scores:
Gap Costs:
History 

        

        

        
Previous result is not found.



  Phylogenetic Tree
- Phylogenetic Tree Tutorial
- About using tools
Select Accessions:
Display mode:     
MoveTo & Select Acc:
Hide

Show
Select Region:
Feature ID:    
Chromosome:  
Position:    -    
* Maximum size is 20,000 bp
Variant Filter: Quality:  >=  
DEPTH:  >=  

Note: It preferentially outputs variant type (ALT) allele. DEL-gap alignment regions are removed.
If GT is "0/1", outputs ambiguous base(IUPAC) of REF and ALT. (SNP only. ex. C/T = Y)
If GT is "1/2"(hetero without REF), outputs ambiguous base of two ALT alleles. (SNP/SNP only)
If the tree is not displayed correctly, please change the sample "Name" to "ID" in AccessionManager.

OS01t0100100-01 Phylogenetic Analysis
Range of color gradient Color definition
SNP

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Min : ▓ 
INDEL

Max: ▓ 

Min : ▓ 
DEPTH

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Min : ▓ 

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Note: The selected settings are applied to each block. If the minimum SNP and INDEL value is >1, the value is rounded-up to 1.
  Primer design
  • Run Primer3
  • Exporting sequence
- Primer design Tutorial
- About using tools
Settings
Target:
 :  -   
* Maximum size of  target + flanking region is 50,000 bp
Flanking region (bp):

  
* Maximum size of  target + flanking region is 50,000 bp
Avoid sites around
the target (bp): 		 
Variant sites masking:
Note: Sets the quality threshold for variant sites ("hetero" or "homo"). Those sites are masked as "N".
Quality: ≧  
DEPTH: ≧  
Avoid sites with
"Depth=NA":
Allowed ratio of "DEPTH = NA" accessions : ≤ 
Allowed number of "DEPTH = NA" accessions : ≤ 
General settings
Product size range:   - 
Primer optimum size:  
Primer max size:  
Primer min size:  
Primer optimum TM:  
Primer max TM:  
Primer min TM:  
Max TM diffrence:  
Primer lowercase masking:
e-PCR

Product size range :  -   
Primer max TM : 
Primer min TM : 
Concentration of monovalent cations : 
Concentration of divalent cations : 
Concentration of dNTPs(mM) : 
Annealing oligo concentration(nM) : 
History

Previous result is not found.

Target:
 :  -   
Flanking region (bp):

 
* Maximum size of  target + flanking region is 50,000 bp
Avoid sites around
the target (bp): 		 
Variant sites masking:
Note: Variant sites (regardless "hetero" or "homo") passing thresholds set below will be masked as "N" in the input sequence.
Quality: ≧ 
DEPTH: ≧ 

  Exporting FASTA
Select Region:
Feature ID:     export as
Chromosome: 
Position:   -    
* Maximum size is 200,000 bp
Variant Filer: Quality:  >=  
DEPTH:  >=  
Line break (bp):   =    * Use 0 for non-breaking.   

Note: The fasta file being exported shows preferentially variant type allele regardless of its genotype "heterozygous or homozygous".
All Accession sequences(DNA) are aligned by gaps and have the same length. Ns in the alignment indicates unmapped site (Depth=0).
If GT is "1/2"(hetero without REF), the first ALT allele is output.

Chromosome:
Position:
  		 -  
    * Maximum size is 200,000 bp
Feature ID:
Variant Filter: Quality:  >=  
DEPTH:  >=  

Leaves number

* If it can not collapse to specified number, it collapses to a close number.

  • Accession list

    • Display mode:     
    MoveTo & Select Acc:

    Hide

    Show


    * Since SystemTree is ON, the above sort order is not reflected in track.

  • Accession title

    • View: ID or NAME  Subtitle  Width 
    Color: Colors for each groups  Destination group  Color  ▓ 

  • System tree (Whole genome tree)

    		•
    * SystemTree is not used.
    Style: Type   Correction   Sort by  
    View: Width  
    Threshold of auto node collapsing:
    Comparison with TreeHeight: ***  

  • Recovery list (original)

    •   Search
    Keyword  
    (eg. Os01g0100100-01) * The keyword must have at least 3 characters.

     


    Position  
    ID/Name
    		 
    History
    : Quality of variant
    : Depth of all reads
    : Depth of alternative allele
    SnpEff Variant impact:
           

    To learn more about using TASUKE, visit this page.
  • Display Modes

    • Modes shown below can be changed at menu bar.
    There are two modes for displaying variant: "block" unit and "one-base" unit.
    The "block" mode has two variant color modes: "Frequency" and "SnpEff".
    The "one-base" mode has three color modes: "Allele", "GT", and "SnpEff".
    Variant only.
    "Block" is shown variant frequency in blue gradation. In "one-base", each variant is displayed as a bar.
    Regions with no mapped reads are highlighted in yellow.
    DEPTH.
    Average depth value of the block is shown in gray gradient.
    Depth & Varaint.
    Variant is shown as inner box with the depth as background.
  • Mouse
    		•
    Drag Horizontally on the map.
    Double click to zoom in around the clicked point.
    Click on an accession name for changing the reference.
    Click again to restore the reference to the default setting.
  • Shortcut keys
    		•
     Movements 
    ← Move to left window
    → Move to right window
    <space> Move to right window
    <home> Move to head of current chr
    <end> Move to tail of current chr
    ↑ Zoom in
    <+> Zoom in
    <-> Zoom out
    ↓ Zoom out
     Display modes 
    p Show/Hide DEPTH
    s Show/Hide SNP
    i Show/Hide INDEL
    d Show/Hide indicator on map
    n Show/Hide DEPTH=0
    e On/Off SnpEff
    r On/Off SystemTree
    b On/Off Block mode
    l On/Off Cursor lines
    h This manual page.
    Keyword:
    You will lose just all of your settings.
    (Data won't be deleted.)
    * It will be reloaded when restore.
    ID NAME VARIETY SUB VARIETY ORIGIN ORIGIN2 TYPE OTHER1 OTRER2

    * It will be reloaded.
    : Number of blocks
    : Block Height
    : Block Width

  • ▓ MODIFIER
    • INTERGENIC
    • UPSTREAM
    • DOWNSTREAM
    • UTR_5_PRIME
    • UTR_3_PRIME
    • REGULATION
    • INTRAGENIC
    • EXON
    • GENE
    • INTRON_CONSERVED
    • INTRON
    • INTERGENIC_CONSERVED
  • ▓ LOW
    • SYNONYMOUS_START
    • NON_SYNONYMOUS_START
    • START_GAINED
    • SYNONYMOUS_CODING
    • SYNONYMOUS_STOP
    • CDS
    • TRANSCRIPT
    • CHROMOSOME_LARGE_DUPLICATION
    • SPLICE_SITE_REGION
    • SPLICE_SITE_BRANCH
    • SPLICE_SITE_BRANCH_U12
    • MICRO_RNA
    • NON_SYNONYMOUS_STOP
  • ▓ MODERATE
    • NON_SYNONYMOUS_CODING
    • CODON_CHANGE
    • CODON_INSERTION
    • CODON_CHANGE_PLUS_CODON_INSERTION
    • CODON_DELETION
    • CODON_CHANGE_PLUS_CODON_DELETION
    • UTR_5_DELETED
    • UTR_3_DELETED
    • CHROMOSOME_LARGE_INVERSION
    • NEXT_PROT
  • ▓ HIGH
    • SPLICE_SITE_ACCEPTOR
    • SPLICE_SITE_DONOR
    • START_LOST
    • EXON_DELETED
    • FRAME_SHIFT
    • STOP_GAINED
    • STOP_LOST
    • RARE_AMINO_ACID
    • CHROMOSOME_LARGEDELETION
    • EXON_DELETED_PARTIAL
    • EXON_DUPLICATION
    • EXON_DUPLICATION_PARTIAL
    • EXON_INVERSION
    • EXON_INVERSION_PARTIAL
    • GENE_DELETED
    • GENE_DUPLICATION
    • GENE_FUSION
    • GENE_FUSION_HALF
    • GENE_FUSION_REVERESE
    • GENE_REARRANGEMENT
    • PROTEIN_PROTEIN_INTERACTION_LOCUS
    • PROTEIN_STRUCTURAL_INTERACTION_LOCUS
    • TRANSCRIPT_DELETE
  • ▓ MODIFIER
    • intergenic_region
    • upstream_gene_variant
    • downstream_gene_variant
    • 5_prime_utr_variant
    • 3_prime_utr_variant
    • regulatory_region_variant
    • intragenic_variant
    • gene_variant
    • exon_variant
    • conserved_intron_variant
    • intron_variant
    • conserved_intergenic_variant
    • coding_sequence_variant
    • miRNA
    • non_coding_transcript_exon_variant
    • non_coding_transcript_variant
    • transcript_variant
    • sequence_feature
  • ▓ LOW
    • start_retained
    • initiator_codon_variant
    • synonymous_variant
    • stop_retained_variant
    • splice_region_variant
    • 5_prime_UTR_prematurestart_codon_gain_variant
    • 5_prime_UTR_premature_start_codon_gain_variant
    • start_codon_gain_variant
  • ▓ MODERATE
    • missense_variant
    • inframe_insertion
    • inframe_deletion
    • disruptive_inframe_insertion
    • disruptive_inframe_deletion
    • 5_prime_utr_truncation
    • 3_prime_utr_truncation
  • ▓ HIGH
    • splice_acceptor_variant
    • splice_donor_variant
    • start_lost
    • exon_loss_variant
    • frameshift_variant
    • stop_gained
    • stop_lost
    • rare_amino_acid_variant
    • duplication
    • inversion
    • feature_ablation
    • gene_fusion
    • bidirectional_gene_fusion
    • rearranged_at_DNA_level
    • protein_protein_contact
    • structural_interaction_variant
    • chromosome

    • What is SnpEff?
      GWAS
    Select phenotype
    Select
    chromosome
    Filter by SnpEff Impact level (combine with "OR")
    Sort by