Author: Pandya, Gagan A.; Holmes, Michael H.; Sunkara, Sirisha; Sparks, Andrew; Bai, Yun; Verratti, Kathleen; Saeed, Kelly; Venepally, Pratap; Jarrahi, Behnam; Fleischmann, Robert D.; Peterson, Scott N.
Title: A bioinformatic filter for improved base-call accuracy and polymorphism detection using the Affymetrix GeneChip® whole-genome resequencing platform Document date: 2007_11_15
ID: 16tii0ha_20
Snippet: In general, the DNA sequence of query strains is not known. Therefore, it is not possible to identify locations that are subject to alternate homology effects with total confidence. However, an underlying assumption of the resequencing method is that the query DNA is similar to the reference sequence represented on the chip. Our approach to the problem of the alternate homology effect exploits this assumption. For each SNP observed in the raw res.....
Document: In general, the DNA sequence of query strains is not known. Therefore, it is not possible to identify locations that are subject to alternate homology effects with total confidence. However, an underlying assumption of the resequencing method is that the query DNA is similar to the reference sequence represented on the chip. Our approach to the problem of the alternate homology effect exploits this assumption. For each SNP observed in the raw results, we search for any alternate sequences within the reference sequence that could account for the SNP call. The difference in binding energy between the alternate (SNP) sequence and the reference sequence is used to differentiate between likely artifacts and genuine SNPs. (Calculated binding energy is a much more sensitive predictor of actual binding potential than Tm.)
Search related documents:
Co phrase search for related documents- chip represent and genuine snp: 1
- chip represent and homology effect: 1
- chip represent and reference sequence: 1, 2, 3
- chip represent and SNP sequence: 1
- chip represent reference sequence and dna sequence: 1
- chip represent reference sequence and genuine snp: 1
- chip represent reference sequence and homology effect: 1
- chip represent reference sequence and reference sequence: 1
- chip represent reference sequence and SNP sequence: 1
- dna sequence and genuine snp: 1, 2, 3
- dna sequence and homology effect: 1, 2, 3
- dna sequence and query dna: 1
- dna sequence and reference sequence: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16
- dna sequence and SNP sequence: 1, 2, 3, 4, 5
- genuine snp and homology effect: 1
- genuine snp and reference sequence: 1, 2
- genuine snp and SNP sequence: 1, 2
- genuine snp and underlying assumption: 1
- homology effect and query dna: 1
Co phrase search for related documents, hyperlinks ordered by date