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Related Concept Videos

pre-mRNA Processing02:01

pre-mRNA Processing

In eukaryotic cells, transcripts made by RNA polymerase are modified and processed before exiting the nucleus. Unprocessed RNA is called precursor mRNA or pre-mRNA to distinguish it from mature mRNA.
Once about 20-40 ribonucleotides have been joined together by RNA polymerase, a group of enzymes adds a “cap” to the 5’ end of the growing transcript. In this process, a 5’ phosphate is replaced by modified guanosine that has a methyl group attached to it (7-Methyl guanosine). This 5’ cap helps the...
Pre-mRNA Processing02:01

Pre-mRNA Processing

In eukaryotic cells, transcripts made by RNA polymerase are modified and processed before exiting the nucleus. Unprocessed RNA is called precursor mRNA or pre-mRNA to distinguish it from mature mRNA.
Once about 20-40 ribonucleotides have been joined together by RNA polymerase, a group of enzymes adds a “cap” to the 5’ end of the growing transcript. In this process, a 5’ phosphate is replaced by modified guanosine that has a methyl group attached to it (7-Methyl guanosine). This 5’ cap helps the...
Next-generation Sequencing03:00

Next-generation Sequencing

The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features.
Transfer RNA Synthesis02:36

Transfer RNA Synthesis

One of the unique features of tRNA is the presence of modified bases. In some tRNAs, modified bases account for nearly 20% of the total bases in the molecule. Altogether, these unusual bases protect the tRNA from enzymatic degradation by RNases.
Each of these chemical modifications is carried by a specific enzyme, post-transcription. All of these enzymes have unique base and site-specificity. Methylation, the most common chemical modification, is carried by at least nine different enzymes, with...
Pre-mRNA Processing: Modification of pre-mRNA Ends01:35

Pre-mRNA Processing: Modification of pre-mRNA Ends

In eukaryotic cells, transcripts made by RNA polymerase are modified and processed before exiting the nucleus. Unprocessed RNA is called precursor mRNA or pre-mRNA to distinguish it from mature mRNA.
Once about 20-40 ribonucleotides have been joined together by RNA polymerase, a group of enzymes adds a cap to the 5' end of the growing transcript. In this process, a 5' phosphate is replaced by modified guanosine that has a methyl group attached (7-methyl guanosine). This 5' cap helps the cell...
RNA-seq03:21

RNA-seq

RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while microarray-based...

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Introductory Analysis and Validation of CUT&#38;RUN Sequencing Data
04:58

Introductory Analysis and Validation of CUT&RUN Sequencing Data

Published on: December 13, 2024

EST processing: from trace to sequence.

Ralf Schmid1, Mark Blaxter

  • 1Department of Biochemistry, University of Leicester, Leicester, UK.

Methods in Molecular Biology (Clifton, N.J.)
|March 12, 2009
PubMed
Summary
This summary is machine-generated.

This study introduces a Perl-based software pipeline for processing expressed sequence tag (EST) data. The tool facilitates the conversion of sequence chromatograms into annotated gene objects for small to medium-sized projects.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Expressed Sequence Tag (EST) projects commonly require converting sequence chromatograms into annotated sequence objects.
  • Existing methods may not be optimal for small- to medium-sized EST datasets.

Purpose of the Study:

  • To present a modular software pipeline for efficient processing and analysis of EST data.
  • To facilitate the conversion of raw sequence data into curated gene objects and facilitate public repository submission.

Main Methods:

  • Development of a modular software pipeline using Perl scripts.
  • Implementation of the trace2dbest module for processing trace files and preparing data for dbEST submission.
  • Utilization of the PartiGene module for clustering, assembly into unigenes, and database organization.

Main Results:

  • The software pipeline effectively processes sequence chromatograms from various sequencing platforms.
  • It enables the organization of EST data into a relational database, forming putative gene objects or unigenes.
  • Tools for annotation and web accessibility are provided, enhancing data utility.

Conclusions:

  • The described software pipeline offers a robust and efficient solution for EST data management.
  • It is particularly beneficial for small- to medium-sized EST projects, streamlining bioinformatics workflows.
  • The pipeline supports data submission to public repositories and enhances accessibility for further research.