Related Experiment Videos
Identification of protein coding regions by database similarity search
1National Center for Biotechnology Information, National Library of Medicine, Bethesda, Maryland 20894-0001.
Nature Genetics
|March 1, 1993
Summary
BLASTX reliably identifies reading frames in nucleotide sequences, even with typical data errors. This protein database search tool is crucial for large-scale sequencing projects to detect homologous coding regions early.
Area of Science:
- Bioinformatics
- Genomics
- Computational Biology
Background:
- Sequence similarity suggests homologous coding regions, even in distantly related genes.
- Identifying homologous coding regions is vital for understanding gene function and evolution.
Purpose of the Study:
- To characterize the sensitivity of the BLASTX program to errors and sequence divergence.
- To evaluate BLASTX's effectiveness in identifying homologous coding regions from nucleotide sequences.
Main Methods:
- BLASTX was used to conceptually translate nucleotide query sequences.
- Protein database searches were performed to identify homologous regions.
- The sensitivity of BLASTX to substitution, insertion, and deletion errors was analyzed.
Main Results:
- BLASTX reliably identified reading frames with up to 1% query errors.
- This error rate is typical for primary sequence data.
- BLASTX demonstrated robustness against sequence divergence.
Conclusions:
- BLASTX is effective for detecting homologous coding regions in nucleotide sequences.
- The program is suitable for large-scale sequencing projects due to its error tolerance.
- Early application of BLASTX is recommended for optimal results in error-prone data.