Related Experiment Video
Updated: Aug 11, 2026
09:58
Using RNA-sequencing to Detect Novel Splice Variants Related to Drug Resistance in In Vitro Cancer Models
Published on: December 9, 2016
Spidey: a tool for mRNA-to-genomic alignments
S J Wheelan1, D M Church, J M Ostell
1National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA. wheelan@ncbi.nlm.nih.gov
Genome Research
|November 3, 2001
Summary
We created Spidey, a fast computer program for aligning spliced sequences to genomes. It accurately handles noisy data like alternative splicing and errors, making it a reliable tool for genomic research.
Area of Science:
- Bioinformatics
- Computational Biology
- Genomics
Background:
- Aligning complementary DNA (cDNA) or messenger RNA (mRNA) sequences to genomic DNA is crucial for gene identification and analysis.
- Existing alignment tools may struggle with complexities such as alternative splicing, polymorphisms, sequencing errors, and evolutionary divergence.
Purpose of the Study:
- To develop and evaluate a novel computer program, Spidey, for accurate and efficient spliced sequence alignment to genomic sequences.
- To assess Spidey's performance in handling various data complexities and compare it with existing alignment tools.
Main Methods:
- Development of a computer program utilizing local alignment algorithms and heuristics to achieve global spliced alignments.
- Application of Spidey for aligning reference sequences to genomic sequences, including the draft human genome.
- Utilizing Spidey for aligning mRNA sequences to gene clusters and cross-species genomic alignment (mouse mRNA to human genome).
Main Results:
- Spidey demonstrates the ability to produce reliable spliced alignments rapidly.
- The program effectively handles noisy sequence data, including alternative splicing, polymorphisms, sequencing errors, and evolutionary divergence.
- Comparative analysis shows Spidey performs competitively against other spliced alignment programs within reasonable timeframes.
Conclusions:
- Spidey is a robust and efficient tool for spliced sequence alignment.
- Its capability to manage data complexities makes it valuable for diverse genomic research applications.
- Spidey offers a reliable and timely solution for aligning sequences to genomic data.
Related Concept Videos
01:32RNA Splicing
Splicing is the process by which eukaryotic RNA is edited before its translation into protein. The RNA strand transcribed from eukaryotic DNA is called the primary transcript. The primary transcripts that become mRNAs are called precursor messenger RNAs (pre-mRNAs). Eukaryotic pre-mRNA contains alternating sequences of exons and introns. Exons are nucleotide sequences that code for proteins, whereas introns are the non-coding regions. In RNA splicing, introns are removed and exons are bonded...
01:32RNA Splicing
Splicing is the process by which eukaryotic RNA is edited before its translation into protein. The RNA strand transcribed from eukaryotic DNA is called the primary transcript. The primary transcripts that become mRNAs are called precursor messenger RNAs (pre-mRNAs). Eukaryotic pre-mRNA contains alternating sequences of exons and introns. Exons are nucleotide sequences that code for proteins, whereas introns are the non-coding regions. In RNA splicing, introns are removed and exons are bonded...
02:54Evolutionary Relationships through Genome Comparisons
Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
02:34DNA Microarrays
Microarrays are high-throughput and relatively inexpensive assays that can be automated to analyze large quantities of data at a time. They are used in genome-wide studies to compare gene or protein expression under two varied conditions, such as healthy and diseased states. Microarrays consist of glass or silica slides on which probe molecules are covalently attached through surface functionalization. Most commonly, the slides are prepared through the chemisorption of silanes to silica...
01:57Sanger Sequencing
DNA sequencing is a fundamental technique that is routinely used in the biological sciences. This method can be applied to a range of questions at different scales - from the sequencing of a cloned DNA fragment or the study of a mutation in a gene up to whole-genome sequencing. However, despite the widespread use of sequencing today, it was not until 1977 that Fredrick Sanger and his collaborators developed the chain-termination method to decode DNA sequences. It relies on the separation of a...
03:21RNA-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...
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while microarray-based...