SimuSCoP: reliably simulate Illumina sequencing data based on position and context dependent profiles

SimuSCoP: reliably simulate Illumina sequencing data based on position and context dependent profiles

Background: Some simulators have been developed to mimic generation sequencing data by including such famous error base substitutions and indels. However, they can be degraded by the practicality of functional limitations and runtime. Especially, contextual information and genomic position are not effectively used to reliably characterize the basic substitution patterns, as well as the position and contextual differences of Phred quality score was not fully investigated. Thus, bioinformatics tools more effectively and efficiently is needed.


Results: Here, we introduce a new tool, SimuSCoP, reliably mimic the complex of DNA sequencing data. Base substitution patterns and the statistical behavior Illumina sequencing data quality scores are fully explored and integrated into the simulation model to reliably emulate dataset for different applications. In addition, integrated and easy to use pipes used in SimuSCoP to facilitate simulation of end-to-end from complex samples, and high runtime efficiency is achieved by implementing multithreading tools to run with low memory consumption. These features allow SimuSCoP to obtain substantial improvements in reliability, functionality, practicality and efficiency runtime.

This tool is comprehensively evaluated in various aspects including the consistency of the profile, simulation genomic variation and complex tumor samples, and the results show the advantages of SimuSCoP over existing tools.
Conclusion: SimuSCoP, new bioinformatics tool developed to study an informative profile of sequencing data real and complex data reliably mimic the introduction of genomic variations. We believe that the work presented will catalyze new development of the downstream bioinformatics methods to analyze the sequencing data. The whole genome sequence (WGS) data can change our ability for the individual attributes of the source population.

However, an efficient method of data mining is not developed yet. We present a method multilokus minimum distance (MMD) which quickly dealing with large data sets and methods to optimally choose locus. It is applied to the data to determine the source kampilobakteriosis WGS human, geographical origin of diverse biological species including humans and proteomics of data to classify breast cancer tumors

 SimuSCoP: reliably simulate Illumina sequencing data based on position and context dependent profiles
SimuSCoP: reliably simulate Illumina sequencing data based on position and context dependent profiles

Reinterpret the data sequencing sheep muscle-specific RNA strand featuring spacious 3’UTR extension

The more complex the 3 ‘UTR in higher organisms may have the function of increasing post-transcriptional gene regulation. More recently RNA sequencing technology has provided us with the possibility to capture the landscape of the 3 ‘UTR full of different species and cells. However, no systematic analysis related to sheep 3 ‘UTR has been done. Here, we perform a detailed analysis of the 3 ‘UTR with the main objective to identify the intact 3’ UTR landscape in sheep muscle of three stages of development.

Based on the strand-specific RNA sequencing (ssRNA-seq) the data, we found that thousands of genes in sheep muscle kept after UTR is transcribed from the genome reference (Oar_v4.0). More than 66% of the 3 ‘UTR extensions show trends similar expressions with their upstream exon genes. This extension 3 ‘UTR very enriching thousands of conserved microRNA binding sites. 3 ‘UTR RNA-related extensions PFKM (PuaRNA) is estimated to come from the 3’ UTR of PFKM.

TBE-Buffer 5X for DNA Sequencing

40121072-2 500 mL
EUR 44.84

TBE-Buffer 5X for DNA Sequencing

40121072-3 1 L
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TBE-Buffer 5X for DNA Sequencing

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EUR 192.14

EpiNext Bisulfite Sequencing Kit (Illumina)

P-1056
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  • 24 Reactions
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pOET Sequencing Primers

GWB-200100 2 x 100 ul Ask for price

SequaGel Sequencing System 1L Kit - 1KIT

NAT1136 1KIT
EUR 187.65

SequaGel Sequencing System 2.2L Kit - EACH

NAT1138 EACH
EUR 318.6

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ESEQ1100-SYS ea
EUR 1842

Sequencing Grade Chymotrypsin

RE013 100ug
EUR 309

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Trypin for Mass & Sequencing

T9600-025 25ug
EUR 174

Trypin for Mass & Sequencing

T9600-100 100ug
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Trypin for Mass & Sequencing

T9600-112 12x100ug
EUR 1988.4

Trypin for Mass & Sequencing

T9600-400 4x100ug
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Sequencing Grade V8 Protease

RE014 50ug
EUR 209

Chymotrypsin for Sequencing grade

C4001-010 4x25ug
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Chymotrypsin for Sequencing grade

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EUR 343.2

Sequencing Grade Modified Trypsin

RE012 100ug
EUR 229

Sequencing Grade Carboxypeptidase B

RE011 100ug
EUR 99

ACES Sequencing Buffer 10X, pH 7.7

21420000-1 1 L
EUR 138.62

ACES Sequencing Buffer 10X, pH 7.7

21420000-2 4 L
EUR 456.17

Bovine Trypsin Purified Sequencing Grade

IBOTRYSEQ100UG each
EUR 148
Description: Bovine Trypsin Purified Sequencing Grade

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IBOTRYSEQ1MG each
EUR 765
Description: Bovine Trypsin Purified Sequencing Grade

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EUR 419
Description: Bovine Trypsin Purified Sequencing Grade

MagaDye™ 4 Color Sanger Sequencing Terminator Kit

17068 5 nmoles
EUR 2091

Bovine Trypsin Purified Sequencing Grade Lyophilized

IBOTRYSEQLY100UG each
EUR 130
Description: Bovine Trypsin Purified Sequencing Grade Lyophilized

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EUR 640
Description: Bovine Trypsin Purified Sequencing Grade Lyophilized

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IBOTRYSEQLY400UG each
EUR 344
Description: Bovine Trypsin Purified Sequencing Grade Lyophilized

Genorise® Customized PCR primers for cloning and sequencing

GR108023 2 nmol
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Bovine Alpha Chymotrypsin 3X Crystallized TLCK Treated Sequencing Grade

IBOCHYTLCKSG100UG each
EUR 297
Description: Bovine Alpha Chymotrypsin 3X Crystallized TLCK Treated Sequencing Grade

Bacteria-Derived Clostripain (Endoproteinase-Arg-C) Sequencing Grade Purified

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Description: Bacteria-Derived Clostripain (Endoproteinase-Arg-C) Sequencing Grade Purified

Bacteria-Derived V8 Protease (Endoprotease Glu-C) Sequencing Grade Lyophilized

IBCTV8SEQLY250UG each
EUR 784
Description: Bacteria-Derived V8 Protease (Endoprotease Glu-C) Sequencing Grade Lyophilized

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Description: Bacteria-Derived V8 Protease (Endoprotease Glu-C) Sequencing Grade Lyophilized

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Cell Cycle & DNA Content Solution

PI/RNASE 200 test
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Description: PI/RNAse

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GC-Rich Sequence DNA-Binding Factor 1 (GCFC1) Antibody

20-abx217653
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DLSM0247 100 Assays Ask for price
Description: Detection cell cycle and cell proliferation using flow cytometry.

Cell Cycle Assay Kit

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Cell Cycle Assay Kit

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E051008 5x50ug
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Description: Available in various conjugation types.

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Description: Abbkine Cell Cycle Staining Kit provides a convenient and accurate determination of the percentage of cells in each phase of the cell cycle.

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K920-100 each
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Cell Cycle Phosphorylation Sampler Kit

E051007 5x50ug
EUR 655
Description: Available in various conjugation types.

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ELI-39072h 96 Tests
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Cell Cycle Assay Kit (Red Fluorescence)

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EUR 128

Cell Cycle Assay Kit (Red Fluorescence)

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Cell Cycle Assay Kit (Red Fluorescence)

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Description: Cell Cycle

Mouse G-Rich Sequence Factor 1 (GRSF1) ELISA Kit

abx389463-96tests 96 tests
EUR 1093.2

Human G-Rich Sequence Factor 1 (GRSF1) ELISA Kit

abx384974-96tests 96 tests
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SFRS17A (untagged)-Human DNA segment on chromosome X and Y (unique) 155 expressed sequence (cDNA clone MGC:39904 IMAGE:5217247), complete cds

SC123528 10 µg Ask for price

Cell Cycle Assay Kit (Blue Fluorescence)

E-CK-A353-100Assays 100Assays
EUR 128
Description: Cell Cycle

Cell Cycle Assay Kit (Blue Fluorescence)

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EUR 45
Description: Cell Cycle

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EUR 78
Description: Cell Cycle

Cell Cycle Assay Kit (Blue Fluorescence)

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Description: Cell Cycle

Lenti ORF clone of Human DNA segment on chromosome 4 (unique) 234 expressed sequence (D4S234E), transcript variant 2, mGFP tagged

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Lenti-ORF clone of PAXBP1 (Myc-DDK-tagged)-Human GC-rich sequence DNA-binding factor 1 (GCFC1), transcript variant 1

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Cell Cycle Assay Kit (Green Fluorescence)

E-CK-A352-100Assays 100Assays
EUR 128
Description: Cell Cycle

Cell Cycle Assay Kit (Green Fluorescence)

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EUR 45
Description: Cell Cycle

Cell Cycle Assay Kit (Green Fluorescence)

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EUR 78
Description: Cell Cycle

Cell Cycle Assay Kit (Green Fluorescence)

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Description: Cell Cycle

human similar to cDNA sequence BC027382 ELISA Kit

201-12-1889 96 tests
EUR 528
Description: A quantitative ELISA kit for measuring Human in samples from biological fluids.

Human similar to cDNA sequence BC027382 ELISA Kit

GA-E1905HM-48T 48T
EUR 346.8

Human similar to cDNA sequence BC027382 ELISA Kit

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human similar to cDNA sequence BC027382 ELISA Kit

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Single Cell Sequence Specific Amplification Kit

P621-01 200 rxn
EUR 435

Rat Cell Division Cycle 23 ELISA kit

E02C0478-192T 192 tests
EUR 1524
Description: A competitive ELISA for quantitative measurement of Rat Cell Division Cycle 23 in samples from blood, plasma, serum, cell culture supernatant and other biological fluids. This is a high quality ELISA kit developped for optimal performance with samples from the particular species.

Rat Cell Division Cycle 23 ELISA kit

E02C0478-48 1 plate of 48 wells
EUR 624
Description: A competitive ELISA for quantitative measurement of Rat Cell Division Cycle 23 in samples from blood, plasma, serum, cell culture supernatant and other biological fluids. This is a high quality ELISA kit developped for optimal performance with samples from the particular species.

Rat Cell Division Cycle 23 ELISA kit

E02C0478-96 1 plate of 96 wells
EUR 822
Description: A competitive ELISA for quantitative measurement of Rat Cell Division Cycle 23 in samples from blood, plasma, serum, cell culture supernatant and other biological fluids. This is a high quality ELISA kit developped for optimal performance with samples from the particular species.

Pig Cell Division Cycle 23 ELISA kit

E07C0478-192T 192 tests
EUR 1524
Description: A competitive ELISA for quantitative measurement of Porcine Cell Division Cycle 23 in samples from blood, plasma, serum, cell culture supernatant and other biological fluids. This is a high quality ELISA kit developped for optimal performance with samples from the particular species.

Pig Cell Division Cycle 23 ELISA kit

E07C0478-48 1 plate of 48 wells
EUR 624
Description: A competitive ELISA for quantitative measurement of Porcine Cell Division Cycle 23 in samples from blood, plasma, serum, cell culture supernatant and other biological fluids. This is a high quality ELISA kit developped for optimal performance with samples from the particular species.

Pig Cell Division Cycle 23 ELISA kit

E07C0478-96 1 plate of 96 wells
EUR 822
Description: A competitive ELISA for quantitative measurement of Porcine Cell Division Cycle 23 in samples from blood, plasma, serum, cell culture supernatant and other biological fluids. This is a high quality ELISA kit developped for optimal performance with samples from the particular species.

Dog Cell Division Cycle 23 ELISA kit

E08C0478-192T 192 tests
EUR 1524
Description: A competitive ELISA for quantitative measurement of Canine Cell Division Cycle 23 in samples from blood, plasma, serum, cell culture supernatant and other biological fluids. This is a high quality ELISA kit developped for optimal performance with samples from the particular species.

Dog Cell Division Cycle 23 ELISA kit

E08C0478-48 1 plate of 48 wells
EUR 624
Description: A competitive ELISA for quantitative measurement of Canine Cell Division Cycle 23 in samples from blood, plasma, serum, cell culture supernatant and other biological fluids. This is a high quality ELISA kit developped for optimal performance with samples from the particular species.

Dog Cell Division Cycle 23 ELISA kit

E08C0478-96 1 plate of 96 wells
EUR 822
Description: A competitive ELISA for quantitative measurement of Canine Cell Division Cycle 23 in samples from blood, plasma, serum, cell culture supernatant and other biological fluids. This is a high quality ELISA kit developped for optimal performance with samples from the particular species.

Rat Cell Division Cycle 23 ELISA kit

E01A10996 96T
EUR 700
Description: ELISA

Goat Cell Division Cycle 23 ELISA kit

E01A45908 96T
EUR 700
Description: ELISA

Goat Cell Division Cycle 23 ELISA kit

E06C0478-192T 192 tests
EUR 1524
Description: A competitive ELISA for quantitative measurement of Goat Cell Division Cycle 23 in samples from blood, plasma, serum, cell culture supernatant and other biological fluids. This is a high quality ELISA kit developped for optimal performance with samples from the particular species.

Goat Cell Division Cycle 23 ELISA kit

E06C0478-48 1 plate of 48 wells
EUR 624
Description: A competitive ELISA for quantitative measurement of Goat Cell Division Cycle 23 in samples from blood, plasma, serum, cell culture supernatant and other biological fluids. This is a high quality ELISA kit developped for optimal performance with samples from the particular species.

Goat Cell Division Cycle 23 ELISA kit

E06C0478-96 1 plate of 96 wells
EUR 822
Description: A competitive ELISA for quantitative measurement of Goat Cell Division Cycle 23 in samples from blood, plasma, serum, cell culture supernatant and other biological fluids. This is a high quality ELISA kit developped for optimal performance with samples from the particular species.

Rat cell division cycle (CDC) ELISA Kit

NSL1569r 96 Tests
EUR 498

Lenti ORF particles, PAXBP1 (mGFP-tagged)-Human GC-rich sequence DNA-binding factor 1 (GCFC1), transcript variant 1, 200ul, >10^7 TU/mL

RC224365L4V 200 µl Ask for price

Lenti ORF particles, PAXBP1 (mGFP-tagged)-Human GC-rich sequence DNA-binding factor 1 (GCFC1), transcript variant 2, 200ul, >10^7 TU/mL

RC224419L4V 200 µl Ask for price

Human MCL1(Myeloid Cell Leukemia Sequence 1) ELISA Kit

RE2013H-48wells 48 wells
EUR 125.55

Human MCL1(Myeloid Cell Leukemia Sequence 1) ELISA Kit

RE2013H-96wells 96 wells
EUR 179.55

Human Myeloid cell leukemia sequence 1 (MCL1) ELISA Kit

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Human Myeloid cell leukemia sequence 1 (MCL1) ELISA Kit

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Mouse Cell Division Cycle 23 ELISA kit

E01A19737 96T
EUR 700
Description: ELISA

Human Cell Division Cycle 23 ELISA kit

E01A2234 96T
EUR 700
Description: ELISA

Mouse Cell Division Cycle 23 ELISA kit

E03C0478-192T 192 tests
EUR 1524
Description: A competitive ELISA for quantitative measurement of Mouse Cell Division Cycle 23 in samples from blood, plasma, serum, cell culture supernatant and other biological fluids. This is a high quality ELISA kit developped for optimal performance with samples from the particular species.

Mouse Cell Division Cycle 23 ELISA kit

E03C0478-48 1 plate of 48 wells
EUR 624
Description: A competitive ELISA for quantitative measurement of Mouse Cell Division Cycle 23 in samples from blood, plasma, serum, cell culture supernatant and other biological fluids. This is a high quality ELISA kit developped for optimal performance with samples from the particular species.

Mouse Cell Division Cycle 23 ELISA kit

E03C0478-96 1 plate of 96 wells
EUR 822
Description: A competitive ELISA for quantitative measurement of Mouse Cell Division Cycle 23 in samples from blood, plasma, serum, cell culture supernatant and other biological fluids. This is a high quality ELISA kit developped for optimal performance with samples from the particular species.

Human Cell Division Cycle 23 ELISA kit

E01C0478-192T 192 tests
EUR 1524
Description: A competitive ELISA for quantitative measurement of Human Cell Division Cycle 23 in samples from blood, plasma, serum, cell culture supernatant and other biological fluids. This is a high quality ELISA kit developped for optimal performance with samples from the particular species.

Human Cell Division Cycle 23 ELISA kit

E01C0478-48 1 plate of 48 wells
EUR 624
Description: A competitive ELISA for quantitative measurement of Human Cell Division Cycle 23 in samples from blood, plasma, serum, cell culture supernatant and other biological fluids. This is a high quality ELISA kit developped for optimal performance with samples from the particular species.

Human Cell Division Cycle 23 ELISA kit

E01C0478-96 1 plate of 96 wells
EUR 822
Description: A competitive ELISA for quantitative measurement of Human Cell Division Cycle 23 in samples from blood, plasma, serum, cell culture supernatant and other biological fluids. This is a high quality ELISA kit developped for optimal performance with samples from the particular species.

Rat Cell division cycle gene ELISA kit

E02C0720-192T 192 tests
EUR 1524
Description: A competitive ELISA for quantitative measurement of Rat Cell division cycle gene in samples from blood, plasma, serum, cell culture supernatant and other biological fluids. This is a high quality ELISA kit developped for optimal performance with samples from the particular species.

Rat Cell division cycle gene ELISA kit

E02C0720-48 1 plate of 48 wells
EUR 624
Description: A competitive ELISA for quantitative measurement of Rat Cell division cycle gene in samples from blood, plasma, serum, cell culture supernatant and other biological fluids. This is a high quality ELISA kit developped for optimal performance with samples from the particular species.

Rat Cell division cycle gene ELISA kit

E02C0720-96 1 plate of 96 wells
EUR 822
Description: A competitive ELISA for quantitative measurement of Rat Cell division cycle gene in samples from blood, plasma, serum, cell culture supernatant and other biological fluids. This is a high quality ELISA kit developped for optimal performance with samples from the particular species.

Sheep Cell Division Cycle 23 ELISA kit

E01A98202 96T
EUR 700
Description: ELISA

Pig Cell division cycle gene ELISA kit

E07C0720-192T 192 tests
EUR 1524
Description: A competitive ELISA for quantitative measurement of Porcine Cell division cycle gene in samples from blood, plasma, serum, cell culture supernatant and other biological fluids. This is a high quality ELISA kit developped for optimal performance with samples from the particular species.

Pig Cell division cycle gene ELISA kit

E07C0720-48 1 plate of 48 wells
EUR 624
Description: A competitive ELISA for quantitative measurement of Porcine Cell division cycle gene in samples from blood, plasma, serum, cell culture supernatant and other biological fluids. This is a high quality ELISA kit developped for optimal performance with samples from the particular species.

Pig Cell division cycle gene ELISA kit

E07C0720-96 1 plate of 96 wells
EUR 822
Description: A competitive ELISA for quantitative measurement of Porcine Cell division cycle gene in samples from blood, plasma, serum, cell culture supernatant and other biological fluids. This is a high quality ELISA kit developped for optimal performance with samples from the particular species.

Dog Cell division cycle gene ELISA kit

E08C0720-192T 192 tests
EUR 1524
Description: A competitive ELISA for quantitative measurement of Canine Cell division cycle gene in samples from blood, plasma, serum, cell culture supernatant and other biological fluids. This is a high quality ELISA kit developped for optimal performance with samples from the particular species.

In sheep myocytes, myotubes and various networks, PuaRNA expression pattern was positively correlated with that of PFKM. Taken together, this explanation of the 3 ‘UTR greatly extends the range of mammals new post-transcriptional regulatory networks, which have a particular impact on the regulation of muscle development lamb.

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