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GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research–an update.

  June 20, 2021
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GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research–an update.

GenAlEx: Genetic Analysis in Excel is a cross-platform package for population genetic analyses that runs within Microsoft Excel. GenAlEx offers analysis of diploid codominant, haploid and binary genetic loci and DNA sequences. Both frequency-based (F-statistics, heterozygosity, HWE, population assignment, relatedness) and distance-based (AMOVA, PCoA, Mantel tests, multivariate spatial autocorrelation) analyses are provided.
New features include calculation of new estimators of population structure: G'(ST), G”(ST), Jost’s D(est) and F'(ST) through AMOVA, Shannon Information analysis, linkage disequilibrium analysis for biallelic data and novel heterogeneity tests for spatial autocorrelation analysis. Export to more than 30 other data formats is provided. Teaching tutorials and expanded step-by-step output options are included. The comprehensive guide has been fully revised.
METHODS
GenAlEx is written in VBA and provided as a Microsoft Excel Add-in (compatible with Excel 2003, 2007, 2010 on PC; Excel 2004, 2011 on Macintosh). GenAlEx, and supporting documentation and tutorials are freely available at: http://biology.anu

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Site-directed mutagenesis by overlap extension using the polymerase chain reaction.

Overlap extension represents a new approach to genetic engineering. Complementary oligodeoxyribonucleotide (oligo) primers and the polymerase chain reaction are used to generate twoDNA fragments having overlapping ends. These fragments are combined in a subsequent ‘fusion’ reaction in which the overlapping ends anneal, allowing the 3′ overlap of each strand to serve as a primer for the 3′ extension of the complementary strand. The resulting fusion product is amplified further by PCR.
Specific alterations in the nucleotide (nt) sequence can be introduced by incorporating nucleotide changes into the overlapping oligo primers. Using this technique of site-directed mutagenesis, three variants of a mouse major histocompatibility complex class-I gene have been generated, cloned and analyzed. Screening of mutant clones revealed at least a 98% efficiency of mutagenesis. All clones sequenced contained the desired mutations, and a low frequency of random substitution estimated to occur at approx. 1 in 4000 nt was detected. This method represents a significant improvement over standard methods of site-directed mutagenesis because it is much faster, simpler and approaches 100% efficiency in the generation of mutant product.

Crystal structure of the nucleosome core particle at 2.8 A resolution.

The X-ray crystal structure of the nucleosome core particle of chromatin shows in atomic detail how the histone protein octamer is assembled and how 146 base pairs of DNA are organized into a superhelix around it. Both histone/histone and histone/DNA interactions depend on the histone fold domains and additional, well ordered structure elements extending from this motif.
Histone amino-terminal tails pass over and between the gyres of the DNA superhelix to contact neighbouring particles. The lack of uniformity between multiple histone/DNA-binding sites causes the DNA to deviate from ideal superhelix geometry.

Base-calling of automated sequencer traces using phred. I. Accuracy assessment.

The availability of massive amounts of DNA sequence information has begun to revolutionize the practice of biology. As a result, current large-scale sequencing output, while impressive, is not adequate to keep pace with growing demand and, in particular, is far short of what will be required to obtain the 3-billion-base human genome sequence by the target date of 2005.
To reach this goal, improved automation will be essential, and it is particularly important that human involvement in sequence data processing be significantly reduced or eliminated. Progress in this respect will require both improved accuracy of the data processing software and reliable accuracy measures to reduce the need for human involvement in error correction and make human review more efficient. Here, we describe one step toward that goal: a base-calling program for automated sequencer traces, phred, with improved accuracy. phred appears to be the first base-calling program to achieve a lower error rate than the ABI software, averaging 40%-50% fewer errors in the data sets examined independent of position in read, machine running conditions, or sequencing chemistry.

The language of covalent histone modifications

Histone proteins and the nucleosomes they form with DNA are the fundamental building blocks of eukaryotic chromatin. A diverse array of post-translational modifications that often occur on tail domains of these proteins has been well documented.
Although the function of these highly conserved modifications has remained elusive, converging biochemical and genetic evidence suggests functions in several chromatin-based processes. We propose that distinct histone modifications, on one or more tails, act sequentially or in combination to form a ‘histone code’ that is, read by other proteins to bring about distinct downstream events.

UCHIME improves sensitivity and speed of chimera detection

BACKGROUND
Chimeric DNA sequences often form during polymerase chain reaction amplification, especially when sequencing single regions (e.g. 16S rRNA or fungal Internal Transcribed Spacer) to assess diversity or compare populations. Undetected chimeras may be misinterpreted as novel species, causing inflated estimates of diversity and spurious inferences of differences between populations. Detection and removal of chimeras is therefore of critical importance in such experiments.
RESULTS
We describe UCHIME, a new program that detects chimeric sequences with two or more segments. UCHIME either uses a database of chimera-free sequences or detects chimeras de novo by exploiting abundance data.
UCHIME has better sensitivity than ChimeraSlayer (previously the most sensitive database method), especially with short, noisy sequences. In testing on artificial bacterial communities with known composition, UCHIME de novo sensitivity is shown to be comparable to Perseus. UCHIME is >100× faster than Perseus and >1000× faster than ChimeraSlayer.
BACKGROUND
robert@drive5.com
BACKGROUND
Source, binaries and data: http://drive5.com/uchime.
BACKGROUND
Supplementary data are available at Bioinformatics online.

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Lenti ORF clone of 9230110C19Rik (Myc-DDK-tagged) - Mouse RIKEN cDNA 9230110C19 gene (9230110C19Rik)
MR212718L3 10 µg Ask for price

Lenti ORF clone of 4933416C03Rik (Myc-DDK-tagged) - Mouse RIKEN cDNA 4933416C03 gene (4933416C03Rik)
MR212768L3 10 µg Ask for price

Lenti ORF clone of 2310050C09Rik (Myc-DDK-tagged) - Mouse RIKEN cDNA 2310050C09 gene (2310050C09Rik)
MR213070L3 10 µg Ask for price

Lenti ORF clone of 4930578C19Rik (Myc-DDK-tagged) - Mouse RIKEN cDNA 4930578C19 gene (4930578C19Rik)
MR213191L3 10 µg Ask for price

Lenti ORF clone of 4931408C20Rik (Myc-DDK-tagged) - Mouse RIKEN cDNA 4931408C20 gene (4931408C20Rik)
MR213319L3 10 µg Ask for price

Lenti ORF clone of 1700016C15Rik (Myc-DDK-tagged) - Mouse RIKEN cDNA 1700016C15 gene (1700016C15Rik)
MR213349L3 10 µg Ask for price

Lenti ORF clone of 4930562C15Rik (Myc-DDK-tagged) - Mouse RIKEN cDNA 4930562C15 gene (4930562C15Rik)
MR212245L3 10 µg Ask for price

Lenti ORF clone of 4930550C14Rik (Myc-DDK-tagged) - Mouse RIKEN cDNA 4930550C14 gene (4930550C14Rik)
MR213881L3 10 µg Ask for price

Lenti ORF clone of 6820408C15Rik (Myc-DDK-tagged) - Mouse RIKEN cDNA 6820408C15 gene (6820408C15Rik)
MR213995L3 10 µg Ask for price

Lenti ORF clone of 2700062C07Rik (Myc-DDK-tagged) - Mouse RIKEN cDNA 2700062C07 gene (2700062C07Rik)
MR202407L3 10 µg Ask for price

Lenti ORF clone of 1700129C05Rik (Myc-DDK-tagged) - Mouse RIKEN cDNA 1700129C05 gene (1700129C05Rik)
MR202447L3 10 µg Ask for price

Lenti ORF clone of 2210407C18Rik (Myc-DDK-tagged) - Mouse RIKEN cDNA 2210407C18 gene (2210407C18Rik)
MR202499L3 10 µg Ask for price

Lenti ORF clone of 2900092C05Rik (Myc-DDK-tagged) - Mouse RIKEN cDNA 2900092C05 gene (2900092C05Rik)
MR201689L3 10 µg Ask for price

Lenti ORF clone of 1700001C02Rik (Myc-DDK-tagged) - Mouse RIKEN cDNA 1700001C02 gene (1700001C02Rik)
MR202026L3 10 µg Ask for price

Lenti ORF clone of 2210010C04Rik (Myc-DDK-tagged) - Mouse RIKEN cDNA 2210010C04 gene (2210010C04Rik)
MR203116L3 10 µg Ask for price

Lenti ORF clone of 1700018C11Rik (Myc-DDK-tagged) - Mouse RIKEN cDNA 1700018C11 gene (1700018C11Rik)
MR200419L3 10 µg Ask for price

Lenti ORF clone of 4930549C01Rik (Myc-DDK-tagged) - Mouse RIKEN cDNA 4930549C01 gene (4930549C01Rik)
MR201321L3 10 µg Ask for price

Lenti ORF clone of 9530077C05Rik (Myc-DDK-tagged) - Mouse RIKEN cDNA 9530077C05 gene (9530077C05Rik)
MR208319L3 10 µg Ask for price

Lenti ORF clone of 5730559C18Rik (Myc-DDK-tagged) - Mouse RIKEN cDNA 5730559C18 gene (5730559C18Rik)
MR209867L3 10 µg Ask for price

Lenti ORF clone of 4921511C04Rik (Myc-DDK-tagged) - Mouse RIKEN cDNA 4921511C04 gene (4921511C04Rik)
MR206164L3 10 µg Ask for price

Lenti ORF clone of 6030419C18Rik (Myc-DDK-tagged) - Mouse RIKEN cDNA 6030419C18 gene (6030419C18Rik)
MR204012L3 10 µg Ask for price

C730048C13Rik (GFP-tagged) - Mouse RIKEN cDNA C730048C13 gene (cDNA clone MGC:54808 IMAGE:5044850)
MG207692 10 µg Ask for price

C730004C24Rik (GFP-tagged) - Mouse RIKEN cDNA C730004C24 gene (cDNA clone MGC:102487 IMAGE:5132591)
MG207861 10 µg Ask for price

C920006C10Rik (untagged) - Mouse RIKEN cDNA C920006C10 gene (cDNA clone MGC:7643 IMAGE:3495608), (10ug)
MC206470 10 µg Ask for price

C730048C13Rik (untagged) - Mouse RIKEN cDNA C730048C13 gene (cDNA clone MGC:54808 IMAGE:5044850), (10ug)
MC218679 10 µg Ask for price

C730004C24Rik (untagged) - Mouse RIKEN cDNA C730004C24 gene (cDNA clone MGC:102487 IMAGE:5132591), (10ug)
MC218718 10 µg Ask for price

Lenti ORF clone of Cnot2 (mGFP-tagged) - Mouse CCR4-NOT transcription complex, subunit 2 (cDNA clone MGC:70296 IMAGE:5003026)
MR208509L4 10 µg Ask for price

CCRN4L (untagged)-Human cDNA clone MGC:78549 IMAGE:2959976, complete cds
SC122302 10 µg Ask for price

Lenti ORF clone of Cnot2 (Myc-DDK-tagged) - Mouse CCR4-NOT transcription complex, subunit 2 (cDNA clone MGC:70296 IMAGE:5003026)
MR208509L3 10 µg Ask for price

Human Chemokine C-C-Motif Receptor 6 (CCR6) ELISA Kit
SEC014Hu-10x96wellstestplate 10x96-wells test plate
EUR 5677.8
Description: This is Double-antibody Sandwich Enzyme-linked immunosorbent assay for detection of Human Chemokine C-C-Motif Receptor 6 (CCR6) in tissue homogenates, cell lysates and other biological fluids.

Human Chemokine C-C-Motif Receptor 6 (CCR6) ELISA Kit
SEC014Hu-1x48wellstestplate 1x48-wells test plate
EUR 572.76
Description: This is Double-antibody Sandwich Enzyme-linked immunosorbent assay for detection of Human Chemokine C-C-Motif Receptor 6 (CCR6) in tissue homogenates, cell lysates and other biological fluids.

Human Chemokine C-C-Motif Receptor 6 (CCR6) ELISA Kit
SEC014Hu-1x96wellstestplate 1x96-wells test plate
EUR 766.8
Description: This is Double-antibody Sandwich Enzyme-linked immunosorbent assay for detection of Human Chemokine C-C-Motif Receptor 6 (CCR6) in tissue homogenates, cell lysates and other biological fluids.

Human Chemokine C-C-Motif Receptor 6 (CCR6) ELISA Kit
SEC014Hu-5x96wellstestplate 5x96-wells test plate
EUR 3090.6
Description: This is Double-antibody Sandwich Enzyme-linked immunosorbent assay for detection of Human Chemokine C-C-Motif Receptor 6 (CCR6) in tissue homogenates, cell lysates and other biological fluids.

Human Chemokine C-C-Motif Receptor 6 (CCR6) ELISA Kit
4-SEC014Hu
  • Ask for price
  • Ask for price
  • Ask for price
  • 1 plate of 96 wells
  • 5 plates of 96 wells
  • 10 plates of 96 wells
Description: Enzyme-linked immunosorbent assay based on the Double-antibody Sandwich method for detection of Human Chemokine C-C-Motif Receptor 6 (CCR6) in samples from tissue homogenates, cell lysates and other biological fluids with no significant corss-reactivity with analogues from other species.

Mouse Chemokine C-C-Motif Receptor 6 (CCR6) ELISA Kit
SEC014Mu-10x96wellstestplate 10x96-wells test plate
EUR 5834.88
Description: This is Double-antibody Sandwich Enzyme-linked immunosorbent assay for detection of Mouse Chemokine C-C-Motif Receptor 6 (CCR6) in Tissue homogenates, cell lysates and other biological fluids.

Mouse Chemokine C-C-Motif Receptor 6 (CCR6) ELISA Kit
SEC014Mu-1x48wellstestplate 1x48-wells test plate
EUR 585.7
Description: This is Double-antibody Sandwich Enzyme-linked immunosorbent assay for detection of Mouse Chemokine C-C-Motif Receptor 6 (CCR6) in Tissue homogenates, cell lysates and other biological fluids.

Mouse Chemokine C-C-Motif Receptor 6 (CCR6) ELISA Kit
SEC014Mu-1x96wellstestplate 1x96-wells test plate
EUR 785.28
Description: This is Double-antibody Sandwich Enzyme-linked immunosorbent assay for detection of Mouse Chemokine C-C-Motif Receptor 6 (CCR6) in Tissue homogenates, cell lysates and other biological fluids.

Mouse Chemokine C-C-Motif Receptor 6 (CCR6) ELISA Kit
SEC014Mu-5x96wellstestplate 5x96-wells test plate
EUR 3173.76
Description: This is Double-antibody Sandwich Enzyme-linked immunosorbent assay for detection of Mouse Chemokine C-C-Motif Receptor 6 (CCR6) in Tissue homogenates, cell lysates and other biological fluids.

Mouse Chemokine C-C-Motif Receptor 6 (CCR6) ELISA Kit
4-SEC014Mu
  • Ask for price
  • Ask for price
  • Ask for price
  • 1 plate of 96 wells
  • 5 plates of 96 wells
  • 10 plates of 96 wells
Description: Enzyme-linked immunosorbent assay based on the Double-antibody Sandwich method for detection of Mouse Chemokine C-C-Motif Receptor 6 (CCR6) in samples from Tissue homogenates, cell lysates and other biological fluids. with no significant corss-reactivity with analogues from other species.

C730048C13Rik (Myc-DDK-tagged) - Mouse RIKEN cDNA C730048C13 gene (cDNA clone MGC:54808 IMAGE:5044850)
MR207692 10 µg Ask for price

C730004C24Rik (Myc-DDK-tagged) - Mouse RIKEN cDNA C730004C24 gene (cDNA clone MGC:102487 IMAGE:5132591)
MR207861 10 µg Ask for price

Lenti ORF clone of Ccr6 (mGFP-tagged ORF) - Rat chemokine (C-C motif) receptor 6 (Ccr6), (10 ug)
RR205238L4 10 µg Ask for price

IK cDNA Clone
MBS1268335-001mgPlasmid02mLGlycerolStock 0.01mgPlasmid+0.2mLGlycerol-Stock
EUR 330

IK cDNA Clone
MBS1268335-5x001mgPlasmid5x02mLGlycerolStock 5x0.01mgPlasmid+5x0.2mLGlycerol-Stock
EUR 1430

C5 cDNA Clone
MBS1269057-INQUIRE INQUIRE Ask for price

GK cDNA Clone
MBS1269389-001mgPlasmid02mLGlycerolStock 0.01mgPlasmid+0.2mLGlycerol-Stock
EUR 200

GK cDNA Clone
MBS1269389-5x001mgPlasmid5x02mLGlycerolStock 5x0.01mgPlasmid+5x0.2mLGlycerol-Stock
EUR 855

F9 cDNA Clone
MBS1269602-001mgPlasmid02mLGlycerolStock 0.01mgPlasmid+0.2mLGlycerol-Stock
EUR 200

F9 cDNA Clone
MBS1269602-5x001mgPlasmid5x02mLGlycerolStock 5x0.01mgPlasmid+5x0.2mLGlycerol-Stock
EUR 855

XG cDNA Clone
MBS1266151-001mgPlasmid02mLGlycerolStock 0.01mgPlasmid+0.2mLGlycerol-Stock
EUR 200

XG cDNA Clone
MBS1266151-5x001mgPlasmid5x02mLGlycerolStock 5x0.01mgPlasmid+5x0.2mLGlycerol-Stock
EUR 855

CS cDNA Clone
MBS1266646-001mgPlasmid02mLGlycerolStock 0.01mgPlasmid+0.2mLGlycerol-Stock
EUR 200

CS cDNA Clone
MBS1266646-5x001mgPlasmid5x02mLGlycerolStock 5x0.01mgPlasmid+5x0.2mLGlycerol-Stock
EUR 855

MB cDNA Clone
MBS1266714-001mgPlasmid02mLGlycerolStock 0.01mgPlasmid+0.2mLGlycerol-Stock
EUR 200

MB cDNA Clone
MBS1266714-5x001mgPlasmid5x02mLGlycerolStock 5x0.01mgPlasmid+5x0.2mLGlycerol-Stock
EUR 855

GC cDNA Clone
MBS1266850-001mgPlasmid02mLGlycerolStock 0.01mgPlasmid+0.2mLGlycerol-Stock
EUR 200

GC cDNA Clone
MBS1266850-5x001mgPlasmid5x02mLGlycerolStock 5x0.01mgPlasmid+5x0.2mLGlycerol-Stock
EUR 855

C6 cDNA Clone
MBS1267367-001mgPlasmid02mLGlycerolStock 0.01mgPlasmid+0.2mLGlycerol-Stock
EUR 200

C6 cDNA Clone
MBS1267367-5x001mgPlasmid5x02mLGlycerolStock 5x0.01mgPlasmid+5x0.2mLGlycerol-Stock
EUR 855

MB cDNA Clone
MBS1270062-001mgPlasmid02mLGlycerolStock 0.01mgPlasmid+0.2mLGlycerol-Stock
EUR 200

MB cDNA Clone
MBS1270062-5x001mgPlasmid5x02mLGlycerolStock 5x0.01mgPlasmid+5x0.2mLGlycerol-Stock
EUR 855

HP cDNA Clone
MBS1271125-001mgPlasmid02mLGlycerolStock 0.01mgPlasmid+0.2mLGlycerol-Stock
EUR 200
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