Journal: Nucleic Acids Research

Article Title: SeqBuster, a bioinformatic tool for the processing and analysis of small RNAs datasets, reveals ubiquitous miRNA modifications in human embryonic cells

doi: 10.1093/nar/gkp1127

Figure Lengend Snippet: ( A ) Workflow of SeqBuster pipeline showing the architecture and connection of pre-analysis and analysis modules. In the pre-analysis module, raw data are processed for recognition and annotation. Annotation can be performed through the web server that offers the miRNA and miRNA-precursor databases or through a stand-alone version using any custom database. The processed and annotated data are stored in a MySQL database. The web interface permits the analysis of the data using several R-based packages. The output of every analysis is visualized through a Dynamic HTML format and stored in the server or downloaded to the local machine. ( B ) Scheme of the main menu at SeqBuster home page. The different choices offered by each option in the menu are highlighted in light yellow boxes.

Article Snippet: The adapter recognition and removal is performed using the SeqBuster stand-alone version, supporting raw data from Illumina/Solexa and FLX454 technologies (see tutorial 1 for a detailed procedure).

Techniques:

Journal: Nucleic Acids Research

Article Title: SeqBuster, a bioinformatic tool for the processing and analysis of small RNAs datasets, reveals ubiquitous miRNA modifications in human embryonic cells

doi: 10.1093/nar/gkp1127

Figure Lengend Snippet: Percentage of reads with a mismatch at different positions of the reference miRNA detected by SeqBuster, considering two different annotation strategies. Penalty and reward parameters of −3 and 1 (black bars) or −2 and 3 (grey bars) were used. In both strategies a word size of 7 was considered.

Article Snippet: The adapter recognition and removal is performed using the SeqBuster stand-alone version, supporting raw data from Illumina/Solexa and FLX454 technologies (see tutorial 1 for a detailed procedure).

Techniques:

Journal: Nucleic Acids Research

Article Title: SeqBuster, a bioinformatic tool for the processing and analysis of small RNAs datasets, reveals ubiquitous miRNA modifications in human embryonic cells

doi: 10.1093/nar/gkp1127

Figure Lengend Snippet: Summary of the main packages available in SeqBuster IsomiR analysis module. For the three packages, the parameters that can be configured (tutorial 4) and the analysis output are shown. ( A ) ‘IsomiRs by nucleotide position’ package. This example shows 5′-trimming variants involving three positions upstream and three positions downstream of the reference-miRNAs. The output shows the proportion of miRNAs with a trimming variant in a specific position. In the upper bars, the color pattern indicates the proportion of miRNAs showing a specific nucleotide being involved in the trimming variants. The lower bars show the proportion of the isomiRs with respect to the corresponding reference miRNA in a brown color scale, as described in . A list of miRNAs involved in each type of variant is displayed when clicking inside the table. ( B ) ‘IsomiR full description’ package. The output analysis of this example shows a list of some of the miRNAs presenting 5′-trimming variants involving three positions upstream and three positions downstream of the reference-miRNAs. Every cell represents a position. The color pattern on the left half of the cell indicates the type of nucleotide present in the isomiR, and that of the right side the proportion of the isomiR with respect the reference miRNA. ( C ) ‘Nt-substitution pattern’ package. The output analysis of this example shows a table with the number of miRNAs presenting any of the 12 possible nt-substitution events in positions 2–5 of the reference miRNA. A summary table showing the number of miRNA with any of the 12 possible nt-changes significant changes is also represented. The overall nt-substitution pattern occurring in a statistically significant number of miRNAs is shown in another table. The list of miRNAs for each class of nt-substitution can be retrieved by clicking on the summary table.

Article Snippet: The adapter recognition and removal is performed using the SeqBuster stand-alone version, supporting raw data from Illumina/Solexa and FLX454 technologies (see tutorial 1 for a detailed procedure).

Techniques: Variant Assay