Databases

1
Databases
BI420 Introduction to Bioinformatics
Gabor T. Marth
Department of Biology, Boston College marth_at_bc.edu
2
SNP Mining in BAC Overlaps
Human Chromosome
Tiling path of BACs (finished or 5x shotgun)
Clone overlap
Candidate SNP
SNP Marker Map
100 kb
3
BAC overlap mining
inter- intra-chromosomal duplications known
human repeats fragmentary nature of draft data
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
http//genome.wustl.edu/gsc/polybayes
5
BAC overlap mining results
30,000 clones
gtCloneX ACGTTGCAACGT GTCAATGCTGCA
gtCloneY ACGTTGCAACGT GTCAATGCTGCA
25,901 clones (7,122 finished, 18,779 draft with
basequality values)
21,020 clone overlaps (124,356 fragment overlaps)
ACCTAGGAGACTGAACTTACTG
ACCTAGGAGACCGAACTTACTG
6
Database schema
Clone (1) NH0260K08
CLONE id name received
masked 1 NH0260K08 12-25-99 12-26-99 2 NH0407F02 1
2-28-99 01-03-00
Hit (1)
HSP id sense 1 1
HSP (1)
Clone (2) NH0407F02
Hit (2)
ALLELE id hitID nucleotide 1 1 C 2 2 T
HIT id cloneID hspID start end 1 1 1 1 17957 2 2 1
96912 114891
C
Hit (1)
Allele (1)
SNP id submitted 1 01-04-00
SNP (1)
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)