Laboratory Methods in Enzymology: RNA 7.1Overview RNAsequence data may come from many sources (public databases, sequencing data, etc.) and have different file formats (Table 1.1). Before submission to the stru
Two independent steps for regulating the abundance of globin mRNA were observed. On the transcriptional level we have observed that, in contrast to the transcription of globin genes, the transcription rate of non-globin genes is dramatically reduced throughout the period of induction. When the rate...
In this chapter, we discuss the fundamental concepts behind the formulation of genome sequencing as an optimization problem and detail the steps required to solve this problem using metaheuristics. We use Particle Swarm Optimization (PSO), Cuckoo Search (CS), and Gray Wolf Optimizer (GWO), which...
In living cells, the genetic information in DNA is transcribed to RNA which is then translated to produce a peptide chain of defined sequence1. In these transcription–translation processes, elaborate template mechanisms are critical, particularly in the translation from mRNA to peptides. Thus, a ...
We also modified the published split adapter ligation protocol (see Methods) to include selection of cDNA:RNA duplexes away from unextended reverse-transcription primer (which can cause adapter dimers to form in subsequent steps), while bypassing several gel-electrophoresis purification steps....
Biologists have described the sequence patterns of promoters via transcription factor binding sites (TFBSs). However, the flanking sequences of cis-regulatory elements, have long been overlooked and often arbitrarily decided in promoter design. To address this limitation, we introduce DeepSEED, an AI...
Transcription factors (TFs) control transcription by binding to specific regions of DNA called transcription factor binding sites (TFBSs). The identification of TFBSs is a crucial problem in computational biology and includes the subtask of predicting the location of known TFBS motifs in a given DN...
However, most of them include PCR-based amplification steps, generate imperfect repeats, or result in a pool of clones that differ in the number of repeats [6–13]. As a consequence, additional effort is required to identify and isolate clones with the desired length of nucleotide repeats. ...
Profile HMMs were run on theD. vexillumgenome; initial candidates where then subjected to several filtering steps to remove false positive hits: Regions that contain significant candidates by sequence alignments against any of the positive 197 profile HMMs were found. After, the cross validation of ...
quantity that represents it activity. This can be, for example, the equilibrium affinity of an enzyme to its substrate, the transcription rate from a promoter, the modulation of target expression by a small regulatory RNA, etc. The activity is represented in the cell via a fluorescent reporter...