1. Databases BI420 – Introduction to Bioinformatics Gabor T. Marth
Department of Biology, Boston College

2. SNP Mining in BAC Overlaps
Human Chromosome
Tiling path of BACs
(finished or 5x shotgun)
Clone overlap
GATCGGATCTACTCTTCAAAGAGT
GATCGGATCTGCTCTTCAAAGAGT
Candidate SNP
SNP Marker Map
100 kb

3. BAC overlap mining overlap detection
SNP analysis
overlap detection
inter- & intra-chromosomal duplications
known human repeats
fragmentary nature of draft data
candidate SNP predictions

4. Title
NH0260K08
NH0407F02
Section of base-wise alignment with marked-up candidate SNP (alignment displayed with the CONSED sequence viewer)
SNP mark-up tag produced by PolyBayes

5. BAC overlap mining results
~ 30,000 clones
>CloneX
ACGTTGCAACGT
GTCAATGCTGCA
>CloneY
ACGTTGCAACGT
GTCAATGCTGCA
25,901 clones
(7,122 finished, 18,779 draft
with basequality values)
21,020 clone overlaps
(124,356 fragment overlaps)
ACCTAGGAGACTGAACTTACTG
507,152 high-quality candidate SNPs
(validation rate 83-96%)
Marth et al., Nature Genetics 2001
ACCTAGGAGACCGAACTTACTG

6. Database schema C SNP (1) T Clone (1) NH0260K08 Clone (2) NH0407F02
id name received masked
1 NH0260K
2 NH0407F
Hit (1)
HSP (1)
HSP
id sense
1 1
Clone (2)
NH0407F02
Hit (2)
ALLELE
id hitID nucleotide
1 1 C
2 2 T
HIT
id cloneID hspID start end C
Hit (1)
Allele (1)
SNP (1)
SNP
id submitted
Database tables:
CLONE table: Clone attributes and sequence file location
HSP table: Significant pair-wise BLAST similarity
HIT table: Region of a clone that is part of an HSP
SNP table: Candidate SNP attributes
ALLELE table: Attributes of an allele within a SNP T
Hit (2)
Allele (2)