Fasta Fasta Boi Leo E Raphael ((FREE)) Download
Gabriella Kallin
DNA motif promoter enrichment analysis was performed using the Homer software (v4.10) and MEME Suite (v5.1.1). First, sequences for promoter regions (1000kb upstream ATG) of differentially expressed genes were extracted. The resulting fasta files were then used as input to the Homer software to identify enriched DNA motifs. Finally, the identified motifs were also analyzed using the MEME Suite to confirm their statistical significance and obtain their corresponding sequence logos. We manually identified in the list of motif enrichment all the E-box motifs and Circadian E-box motifs. Boxplot were generated using GraphPad Prism version 9.5.1.
High-throughput sequencing has become commonplace in evolutionary studies. Large, rapidly collected genomic datasets are used to capture biodiversity and for monitoring global and national scale disease transmission patterns, among many other applications. Updating homologous sequence datasets with new samples is cumbersome, requiring excessive program runtimes and data processing. We describe Extensiphy, a bioinformatics tool to efficiently update multiple sequence alignments with whole-genome short-read data. Extensiphy performs reference based sequence assembly and alignment in one process while maintaining the alignment length of the original alignment. Input data-types for Extensiphy are any multiple sequence alignment in fasta format and whole-genome, short-read fastq sequences. To validate Extensiphy, we compared its results to those produced by two other methods that construct whole-genome scale multiple sequence alignments. We measured our comparisons by analysing program runtimes, base-call accuracy, dataset retention in the presence of missing data and phylogenetic accuracy. We found that Extensiphy rapidly produces high-quality updated sequence alignments while preventing alignment shrinkage due to missing data. Phylogenies estimated from alignments produced by Extensiphy show similar accuracy to other commonly used alignment construction methods. Extensiphy is suitable for updating large sequence alignments and is ideal for studies of biodiversity, ecology and epidemiological monitoring efforts. 2021 The Authors. Methods in Ecology and Evolution published by John Wiley & Sons Ltd on behalf of British Ecological Society
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