1. CS 6293 AT: Current Bioinformatics HW2 Papers 1
CS 6293 AT: Current Bioinformatics HW2 Papers 1. BLAT--The BLAST-Like Alignment Tool 2. Classification of DNA sequences using Bloom Filters
Course Intructor
Dr. Jianhua Ruan
Presenters
Husnu Narman
Nihat Altiparmak

2. BLAT--The BLAST-Like Alignment Tool
W. James Kent (2002)
UCSC
Cited by 2229(Google Scholar)

3. Brief Information About BLAST
BLAST: Basic Local Allignment Search Tool
Find a gene in different kinds of databases
Divide query to small part words and compare
High Scoring Segments Pairs(HSP)
Scan for exact matches in HSP
Extend exact matches to HSP
Evaluate, handle exceptions, and reports
List all of the HSPs in the database

4. BLAT BLAT: The Blast-Like Alignment Tool
Find a gene in different kinds of databases
Why new search tool?

5. Differences between BLAST and BLAT
Index of Query
Triggers extension one or two hit occur
List of exons sorted by size
BLAT
Index of Database
Triggers extensions any number perfect or near perfect hits
Look up location of a sequence in genome or determine exon structure of a mRNA

6. Classification of DNA sequences using Bloom Filters
Strannheim et al. (2010)
Stockholm, SWEDEN

7. Classification of DNA sequences using Bloom Filters
New generation sequencing technologies
Complex datasets
New efficient, specialized sequence analysis algorithms
Often, only noval sequences required, unnecessary sequences(belonging to a known genome) need to be removed
A new algorithm(FACS) to classify sequences as belonging or not belonging to a reference sequence
Source code available at;

8. Bloom Filter
A memory efficient data structure for testing whether an element is part of a reference set
m bit vector with k hash functions
Never returns a false negative; may however return a false positive
Optimal number of hash functions;
𝑘= 𝑚 𝑛 𝑙𝑛2

9. Example Bloom Filter x y z 1 1 1 1 1 1 1 √ x √ w
𝑚=18, 𝑘=3

10. Method
Bloom filter is created from the reference sequence with desired K-mer and false positive rate.
The query sequences are then classified by using the bloom filter

11. Evaluation
Experimental metagenome dataset(Allander et al. 2005) containing reads
Analysis using human genome as a reference
FACS, BLAT and SSAHA2 compared
31x
21x

12. Evaluation False Positive Rate(Missed)

13. Any Questions?