BiQ_Analyzer - a software tool for DNA methylation analysis

Experiment Documentation Questionnaire


[Experimental Setting]

Experimenter: Christoph Bock

Date of experiment: 29.04.2005

Project name: BiQ_Analyzer Beta Test

Experiment No. / ID: 2





[Sample information]

Organism: yeti horribilis 

Strain or subtype: himalaya

Sex: male

Tissue: heart





[Sequence Location] - IMPORTANT -

Please specify the exact genomic location of the analyzed sequence.

Yeti Genome Draft - Acession No. YETI_123456, bp  100032-100151



Accession number of sequence: YETI_123456

Genome browser link: N/A

Additional position information (if applicable): 



	

[Functional Elements]

Please specify the sequence characteristics by ticking the appropriate box(es).

( ) intergenic

	( ) repetitive element, please specify type (L1, ALU, etc.): 

	( ) upstream (2 - 10 kb upstream of transcriptional start site)

	( ) promoter (2 kb upstream to 500 bp downstream of transcription start site)

(X) exonic

( ) intronic



Does the sequence relate to a gene? Please give its GO name: 

Gene Name: Invisible



[Imprinting]

Are there any allele-specific sequence polymorphisms present in sequence? Please tick.

( ) yes

( ) no



If yes, please give its position and specify the polymorphism in detail: 





[Experimental details]

Which primers where used? Please give their sequences: 



How was the experiment carried out? Please specify the protocol used and any deviations from it (or give a lab notebook cross-reference): 





[Quality control]

Please roughly estimate the quality of your sequences:

( ) very good

( ) good

( ) average

( ) just acceptable

( ) poor



What kind of quality problems are present in the sequences? Please specify type and degree: 





[Free comment (motivation / findings / problems / ...)]

Please use this space to give any additional details relating to the experiment, its motivation, or its results: 

thanks to Reinhold Messner for providing the sample... ;-)





[BiQ_Analyzer Documentation (automatically generated)]

Date of quality check: 29 April 2005

Conversion type: C -> T

Genomic Sequence (original): CCCGGGATCGCTCTCCCAGCAGGTGAAGCCTCGCCATGGACCCTCCCCGTCGGGGCCCCGCGCTGCCCCGCCCGCCCCCAGCCGCTGGCCAAGGCCGCGGTCGCGCAGGCGCAGTGCCGCGTCCCGCCGCCGCCCCGCCCTGCCCGTCGCTGCGGAAGGCGCCGCGCGCAGCAACGCGCACTTCCTCTCCAGGAATCCGCGGAGGGAGCGCAGGCTCGAAGAGCTCCTGGACG

Genomic Sequence (fully converted): TTCGGGATCGTTTTTTTAGTAGGTGAAGTTTCGTTATGGATTTTTTTCGTCGGGGTTTCGCGTTGTTTCGTTCGTTTTTAGTCGTTGGTTAAGGTCGCGGTCGCGTAGGCGTAGTGTCGCGTTTCGTCGTCGTTTCGTTTTGTTCGTCGTTGCGGAAGGCGTCGCGCGTAGTAACGCGTATTTTTTTTTTAGGAATTCGCGGAGGGAGCGTAGGTTCGAAGAGTTTTTGGACG





[BiQ_Analyzer Quality Data (automatically generated)]

List of the sequence identities relative to the genomic sequence (gaps ignored):

Sequence [2]: 91%

Sequence [3]: 99%

Sequence [4]: 100%

Sequence [5]: 100%

Sequence [6]: 100%

Sequence [7]: 100%

Sequence [8]: 100%



List of the sequences' conversion rates:

Sequence [2]: 100%   (67 out of 67)

Sequence [3]: 96%   (66 out of 69)

Sequence [4]: 99%   (68 out of 69)

Sequence [5]: 90%   (62 out of 69)

Sequence [6]: 96%   (66 out of 69)

Sequence [7]: 100%   (69 out of 69)

Sequence [8]: 100%   (69 out of 69)

ClustalW Sequence Pileup


CLUSTAL W (1.83) multiple sequence alignment





Genomic_Sequence     TTCGGGATCGTTTTTTT-AGTAGGTGAAGTTTCGTTATGGATTTTTTTCGTCGGGGTTTC

[2]seq_A.seq         TTCGGGATTGTTTTTTT-AGTAGGTGAAGTTTTGTTATGGATTTTTTTTGTTGGGGTTTC

[3]seq_B.seq         TTTGGGATTGTTTTTTT-AGTAGGTGAAGTTTTGTTATGGATTTTTTTTGTTGGGGTTTT

[4]seq_C.seq         TTCGGGATCGTTTTTTT-AGTAGGTGAAGTTTTGTTATGGATTTTTTTCGTTGGGGTTTC

[5]seq_D.seq         TCCGGGATCGTTTTTTT-AGTAGGTGAAGTTTTGTTATGGATTTTCTTTGTTGGGGTTTT

[6]seq_E.seq         TTTGGGATTGTTTTTTTTAGCAGGTGAAGTTTTGTTATGGATTTTTTTTGTTGGGGTTTT

[7]seq_H.seq         TTCGGGATTGTTTTTTT-AGTAGGTGAAGTTTTGTTATGGATTTTTTTTGTTGGGGTTTC

[8]seq_I.seq         TTTGGGATTGTTTTTTT-AGTAGGTGAAGTTTTGTTATGGATTTTTTTTGTTGGGGTTTT

                     *  ***** ******** ** *********** ************ ** ** ******* 



Genomic_Sequence     G-CGTTGTTTCGTTCGTTTTTAGTCGTTGGTT-AAGGTCGCGGTCGCGTAGGCGTAGTGT

[2]seq_A.seq         G-TGTTGTTTTGTTCGTTTTTTGTTGTTGGTT-AAGGAAAAAA------AAAAATAGTGT

[3]seq_B.seq         G-TGTTGTTTTGTTTGTTTTTAGTTGTTGGTT-AAGGTTGTGGTTGTGTAGCTGTAGTGT

[4]seq_C.seq         G-TGTTGTTTTGTTCGTTTTTAGTCGTTGGTT-AAGGTTGCGGTCGCGTAGGCGTAGTGT

[5]seq_D.seq         G-TGTTGTTTTGTTTGTCCTTAGTCGTTGGTT-AAGGTTGTGGTTGTGTAGGTGTGGTGT

[6]seq_E.seq         GATGTTGTTTCGTTTGTTTCTAGTTGTTGGTTTAAGGTCGTGGTTGTGTAGGCGTAGTGT

[7]seq_H.seq         G-TGTTGTTTTGTTCGTTTTTTGTTGTTGGTT-AAGGTCGCGGTCGCGTAGGCGTAGTGT

[8]seq_I.seq         G-TGTTGTTTTGTTTGTTTTTAGTTGTTGGTT-AAGGTTGTGGTTGTGTAGGTGTAGTGT

                     *  ******* *** **   * ** ******* ****            *    * ****



Genomic_Sequence     CGCGTTTCGTCGTCGTTTCGTTTTGTTCGTCGTTGCGGAAGGCG-TCGCGCGTAGTAACG

[2]seq_A.seq         CGCGTTTCGTCGTCGTTTAGTTTTGTTCGTGGTTGCGGAAGGCGGTTGCGCGTAGTAACG

[3]seq_B.seq         TGTGTTTTGTCGTTGTTTTGTTTTGTTTGTTGTTGTGGATGGTG-TTGTGTGTAGCAGTG

[4]seq_C.seq         CGCGTTCCGTCGTCGTTTCGTTTTGTTCGTTGTTGTGGAAGGTG-TTGCGCGTAGTAATG

[5]seq_D.seq         CGTGTCTTGTCGTCGTTCTGTTTTGTTTGTTGTTGCGGAAGGTG-TTGCGTGTAGCAACG

[6]seq_E.seq         CGCGTTTCGTCGTTGTTTTGTTTTGTTCGTCGTTGCGGAAGGTG-TTGTGCGTAGCAATG

[7]seq_H.seq         CGCGTTTCGTCGTCGTTTTGTTTTGTTCGTCGTTGCGGAAGGCGGTTGCGCGTAGTAACG

[8]seq_I.seq         TGTGTTTTGTTGTTGTTTTGTTTTGTTTGTTGTTGTGGAAGGTG-TTGTGTGTAGTAATG

                      * **   ** ** ***  ******** ** **** *** ** * * * * **** *  *



Genomic_Sequence     CGTATTTTTTTTTT-AGGAATTCGCGGAGGGAGCGTAGGTTCGAAGAGTTTTTGGACG

[2]seq_A.seq         TGTATTTTTTTTTT-AGGAATTAGTGGAGGGAGCGTAGGTTCGAAGAGTTTTTGGACG

[3]seq_B.seq         TGTATTTTTTTTTC-AGGAATTTGTGGAGGGAGTGTAGGTTTGAAGAGCTTTTGGATG

[4]seq_C.seq         CGTATTTTTTTTTT-AGGAATTCGTGGAGGGAGTGTAGGTTCGAAGAGTTTTTGGATG

[5]seq_D.seq         TGTATTTTTTTTTT-AGGAATTCGCGGAGGGAGTGTAGGTTCGAAGAGTTTTTGGACG

[6]seq_E.seq         CGTATTTTTTTTTT-AGGAATTTGTGGAGGGAGTGTAGGTTTGAAGAGTTTTTGGATG

[7]seq_H.seq         TGTATTTTTTTTTT-AGGAATTTGTGGAGGGAGCGTAGGTTCGAAGAGTTTTTGGACG

[8]seq_I.seq         TGTATTTTTTTTTTTAGGAATTTGTGGAGGGAGTGTAGGTTTGAAGAGTTTTTGGATG

                      ************  ******* * ******** ******* ****** ******* *

Derived Methylation Data


Genomic Sequence with numbered CpG dinucleotides:

                                                                                    1             1 1   1 1     1       1 1    1  1  2    2        2  2    2      2   2 2 2       2 3                     3 3        3       3              3 

  1     2                       3               4  5       6  7       8   9         0             1 2   3 4     5       6 7    8  9  0    1        2  3    4      5   6 7 8       9 0                     1 2        3       4              5 

CCCGGGATCGCTCTCCC-AGCAGGTGAAGCCTCGCCATGGACCCTCCCCGTCGGGGCCCCG-CGCTGCCCCGCCCGCCCCCAGCCGCTGGCC-AAGGCCGCGGTCGCGCAGGCGCAGTGCCGCGTCCCGCCGCCGCCCCGCCCTGCCCGTCGCTGCGGAAGGCG-CCGCGCGCAGCAACGCGCACTTCCTCTCC-AGGAATCCGCGGAGGGAGCGCAGGCTCGAAGAGCTCCTGGACG



Methylation data for these CpG dinucleotides (1=methylated, 0=unmethylated, x=unknown):

Sequence_Identifier	CpG_1	CpG_2	CpG_3	CpG_4	CpG_5	CpG_6	CpG_7	CpG_8	CpG_9	CpG_10	CpG_11	CpG_12	CpG_13	CpG_14	CpG_15	CpG_16	CpG_17	CpG_18	CpG_19	CpG_20	CpG_21	CpG_22	CpG_23	CpG_24	CpG_25	CpG_26	CpG_27	CpG_28	CpG_29	CpG_30	CpG_31	CpG_32	CpG_33	CpG_34	CpG_35

[2]seq_A.seq       	1	0	0	0	0	1	0	0	1	0	x	x	x	x	x	1	1	1	1	1	x	1	x	1	1	0	1	1	1	0	x	0	1	1	1

[3]seq_B.seq       	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0

[4]seq_C.seq       	1	1	0	1	0	1	0	0	1	1	0	1	1	1	1	1	1	1	1	1	1	1	0	0	0	0	1	1	0	1	1	0	0	1	0

[5]seq_D.seq       	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	1	0	0	1	0	1	0	1	1	0	1	1

[6]seq_E.seq       	0	0	0	0	0	0	0	1	0	0	1	0	0	0	1	1	1	1	1	0	0	1	1	1	0	0	0	1	0	1	0	0	0	0	0

[7]seq_H.seq       	1	0	0	0	0	1	0	0	1	0	1	1	1	1	1	1	1	1	1	1	0	1	1	1	1	0	1	1	1	0	0	0	1	1	1

[8]seq_I.seq       	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0

Explanation: each '1' corresponds to a methylated C, a '0' corresponds to a an unmethylated C, and an 'x' corresponds to a non-CpG position.

Lollipop-like Representation of Methylation Data

Sorry, only text mode lollipops for now. If more than five people write me an e-mail requesting publication-quality diagrams here I'll give in to public demand and add this to the next release...

[2]seq_A.seq	--I-----O-----------------------O---------------O--O-------I--O-------O---I---------O-----------------------------------I-I----I--I--I-------------I-------I------I---O-I-I-------I-O-----------------------O--------I-------I--------------I-
[3]seq_B.seq	--O-----O-----------------------O---------------O--O-------O--O-------O---O---------O-------------O-O---O-O-----O-------O-O----O--I--O----O--------O--O----O------O---O-O-O-------O-O---------------------O-O--------O-------O--------------O-
[4]seq_C.seq	--I-----I-----------------------O---------------I--O-------I--O-------O---I---------I-------------O-I---I-I-----I-------I-I----I--I--I----I--------I--O----O------O---O-I-I-------O-I---------------------I-O--------O-------I--------------O-
[5]seq_D.seq	--I-----I-----------------------O---------------O--O-------O--O-------O---O---------I-------------O-O---O-O-----O-------I-O----O--I--I----O--------O--O----I------O---O-I-O-------I-O---------------------I-I--------O-------I--------------I-
[6]seq_E.seq	--O-----O-----------------------O---------------O--O-------O--O-------I---O---------O-------------I-O---O-O-----I-------I-I----I--I--O----O--------I--I----I------O---O-O-I-------O-I---------------------O-O--------O-------O--------------O-
[7]seq_H.seq	--I-----O-----------------------O---------------O--O-------I--O-------O---I---------O-------------I-I---I-I-----I-------I-I----I--I--I----O--------I--I----I------I---O-I-I-------I-O---------------------O-O--------I-------I--------------I-
[8]seq_I.seq	--O-----O-----------------------O---------------O--O-------O--O-------O---O---------O-------------O-O---O-O-----O-------O-O----O--O--O----O--------O--O----O------O---O-O-O-------O-O---------------------O-O--------O-------O--------------O-

>Generated with BiQ_Analyzer by Christoph Bock