Journal: Nucleic Acids Research

Article Title: Correction of sequence-dependent ambiguous bases (Ns) from the 454 pyrosequencing system

doi: 10.1093/nar/gku070

Figure Lengend Snippet: N error rates from the pure bacterial cultures used in this study

Article Snippet: Pyrosequencing of the 16S ribosomal RNA gene (16S) has become one of the most popular methods to assess microbial diversity.

Techniques:

Journal: Nucleic Acids Research

Article Title: Correction of sequence-dependent ambiguous bases (Ns) from the 454 pyrosequencing system

doi: 10.1093/nar/gku070

Figure Lengend Snippet: Distributions of N errors in the aligned reads of pure cultures including Rhodococcus sp. RHA1 bphD gene region (Rhodococcus_bphD), P. naphthalenivorans CJ2 bphD gene region (Polaromonas_bphD), P. naphthalenivorans CJ2 nifH gene region (Polaromonas_nifH), Rhodococcus sp. RHA1 16S V1–V3 region (Rhodococcus_16S), R. denitrificans OCh 114 16S V1–V3 region (Roseobacter_16S) and S. epidermidis ATCC 12228 16S V1–V3 region (Staphylococcus_16S). Genomic DNAs of the pure cultures were separately barcoded and amplified, but they were pooled for one sequencing run. The Y-axis unit is N error rate per base.

Article Snippet: Pyrosequencing of the 16S ribosomal RNA gene (16S) has become one of the most popular methods to assess microbial diversity.

Techniques: Amplification, Sequencing

Journal: Nucleic Acids Research

Article Title: Correction of sequence-dependent ambiguous bases (Ns) from the 454 pyrosequencing system

doi: 10.1093/nar/gku070

Figure Lengend Snippet: Sequence motifs of the N errors from different pure cultures and genes

Article Snippet: Pyrosequencing of the 16S ribosomal RNA gene (16S) has become one of the most popular methods to assess microbial diversity.

Techniques: Sequencing

Journal: Nucleic Acids Research

Article Title: Correction of sequence-dependent ambiguous bases (Ns) from the 454 pyrosequencing system

doi: 10.1093/nar/gku070

Figure Lengend Snippet: Analysis of the flow values of the nucleotides around Ns

Article Snippet: Pyrosequencing of the 16S ribosomal RNA gene (16S) has become one of the most popular methods to assess microbial diversity.

Techniques: Standard Deviation

Journal: Nucleic Acids Research

Article Title: Correction of sequence-dependent ambiguous bases (Ns) from the 454 pyrosequencing system

doi: 10.1093/nar/gku070

Figure Lengend Snippet: Distribution of Ns before (red line) and after (blue line) the N correction in the mock community. 16S, 16S V1–V3 region. bphD , bphD gene region. nifH , nifH gene region. The Y-axis unit is N error rate per base.

Article Snippet: Pyrosequencing of the 16S ribosomal RNA gene (16S) has become one of the most popular methods to assess microbial diversity.

Techniques:

Journal: Nucleic Acids Research

Article Title: Correction of sequence-dependent ambiguous bases (Ns) from the 454 pyrosequencing system

doi: 10.1093/nar/gku070

Figure Lengend Snippet: Sequence motifs of the highest N error rate areas from the mock community

Article Snippet: Pyrosequencing of the 16S ribosomal RNA gene (16S) has become one of the most popular methods to assess microbial diversity.

Techniques: Sequencing

Journal: Nucleic Acids Research

Article Title: Correction of sequence-dependent ambiguous bases (Ns) from the 454 pyrosequencing system

doi: 10.1093/nar/gku070

Figure Lengend Snippet: Precision analysis of the N correction using the mock community. 16S V1–V3, bphD and nifH indicate results from 16S V1–V3 region, bphD gene region and nifH gene region, respectively. The left pie graphs indicate the numbers of reads with and without Ns among the total reads. The intermediate pie graphs indicate the numbers of the corrected and uncorrected Ns among the total Ns. The right pie graphs indicate the numbers of truly and falsely corrected Ns among the corrected Ns. The ‘Not matched’ refers to Ns from the reads that were not matched with the reference sequences for the mock community.

Article Snippet: Pyrosequencing of the 16S ribosomal RNA gene (16S) has become one of the most popular methods to assess microbial diversity.

Techniques:

Journal: Nucleic Acids Research

Article Title: Correction of sequence-dependent ambiguous bases (Ns) from the 454 pyrosequencing system

doi: 10.1093/nar/gku070

Figure Lengend Snippet: Comparison of error rates (average values) before and after N correction (from the mock community)

Article Snippet: Pyrosequencing of the 16S ribosomal RNA gene (16S) has become one of the most popular methods to assess microbial diversity.

Techniques: Comparison

Journal: Nucleic Acids Research

Article Title: Correction of sequence-dependent ambiguous bases (Ns) from the 454 pyrosequencing system

doi: 10.1093/nar/gku070

Figure Lengend Snippet: Comparison of the impacts of our N correction method and of the conventional method of removing N-containing reads (removal of reads with Ns) on soil bacterial community composition analysis. The original data indicate the soil bacterial community composition estimated from the 16S V1–V3 amplicon sequences before our N correction method or the removal of N-containing reads was applied.

Article Snippet: Pyrosequencing of the 16S ribosomal RNA gene (16S) has become one of the most popular methods to assess microbial diversity.

Techniques: Comparison, Amplification