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A double-screening method to identify reliable candidate non-synonymous SNPs from chicken EST data
H Kim1, C J Schmidt, K S Decker
1Department of Animal and Food Sciences, University of Delaware, Newark, DE 19716, USA.
Animal Genetics
|July 23, 2003
Summary
Identifying non-synonymous single nucleotide polymorphisms (nsSNPs) in chickens is crucial for understanding genetic variation. A new double-screening method successfully identified 108 candidate nsSNPs from chicken expressed sequence tags.
Area of Science:
- Genomics
- Molecular Biology
- Animal Genetics
Background:
- Non-synonymous single nucleotide polymorphisms (nsSNPs) alter protein function and are key to understanding heritable differences.
- Identifying nsSNPs in chickens is challenging due to limited protein and mRNA sequence data for accurate reading frame determination in expressed sequence tags (ESTs).
Purpose of the Study:
- To develop and apply a robust method for identifying nsSNPs in chicken ESTs.
- To establish a searchable database of chicken SNPs for future research.
Main Methods:
- A double-screening approach combining self- or cross-species protein referencing with the ESTScan program was employed.
- A phred/phrap/polyphred/consed pipeline was used to discover potential SNPs from 23,427 chicken ESTs.
- Candidate nsSNPs were identified from the discovered SNPs using the developed double-screening method.
Main Results:
- A total of 1210 potential SNPs were identified from the chicken ESTs.
- The double-screening method successfully identified 108 candidate nsSNPs.
- A searchable SNP database, chickSNPs, was created, containing both nsSNPs and synonymous SNPs (sSNPs).
Conclusions:
- The developed double-screening method effectively identifies nsSNPs in chicken ESTs, overcoming limitations of insufficient sequence data.
- The chickSNPs database provides a valuable resource for researchers studying chicken genetics and variation.