Related Experiment Video
Updated: Jul 2, 2026
09:10
A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes
Published on: May 22, 2018
Direct mapping and alignment of protein sequences onto genomic sequence
1Department of Intelligence Science and Technology, Graduate School of Informatics, Kyoto University, Yoshida Honmachi, Sakyo-ku, Kyoto 606-8501, Japan. o.gotoh@i.kyoto-u.ac.jp
Bioinformatics (Oxford, England)
|August 30, 2008
Summary
Spaln now aligns protein sequences to genomic data, improving gene prediction accuracy and speed. This tool enhances the analysis of homologous genes, especially for distantly related species.
Area of Science:
- Genomics
- Bioinformatics
- Computational Biology
Background:
- Identifying protein-coding genes is crucial for understanding genomic function.
- Homologous gene sequences improve gene prediction accuracy but existing tools have limitations.
- Protein sequences are more conserved than nucleotide sequences, enabling remote homology detection.
Purpose of the Study:
- To extend the Spaln program to accept protein sequences for gene prediction.
- To enable simultaneous mapping and alignment of multiple protein sequences on large genomic sequences.
- To improve the accuracy and efficiency of gene recognition using protein evidence.
Main Methods:
- Extended the Spaln program to incorporate protein sequence queries.
- Developed methods for simultaneous mapping and alignment of protein sequences on genomic data.
- Evaluated Spaln's performance against conventional Blast search and spliced alignment methods.
Main Results:
- Spaln now accepts both cDNA and protein sequences as queries.
- Spaln achieves significantly higher exon-level and gene-level accuracies compared to existing methods.
- Spaln runs one to two orders of magnitude faster than conventional approaches for similar sequences.
Conclusions:
- The extended Spaln program is a powerful tool for accurate and efficient gene prediction.
- Spaln improves evidence-based gene recognition, particularly for distantly related homologous genes.
- Spaln is available online and its source code is free for academic users.
Related Concept Videos
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...
01:33Proteomics
A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term proteomics...
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term proteomics...
03:36Genome Annotation and Assembly
The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
02:24Ribosome Profiling
Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique helps...
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique helps...
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...
02:26Protein Networks
An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...