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4 Οκτ 2013 (πριν από 3 χρόνια και 8 μήνες)

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Sequence Alignment technology

Chengwei

Lei

Fang Yuan

Saleh

Tamim


Goal


Save time


“PASS
: a Program to Align Short Sequences

Davide

Campagna

et al
. Bioinformatics
(2009
)”



Save money


“Optimal
pooling for genome re
-
sequencing with ultra
-
high
-
throughput short
-
read
technologies,

Iman

Hajirasouliha
, Bioinformatics
(2008)



Keywords in both paper


Reference sequence:


A long Genomic sequence.




Short reads:


Input
short strings.
e.g. ATGCGTAC

Save time


PASS program


PASS, a new algorithm to align short
DNA
sequences
allowing gaps and
mismatches.


The performance of
the program is very
striking both for sensitivity and speed.
For
instance
, gap alignment is achieved hundreds
of times faster
than BLAST
and several times
faster
than SOAP, especially when gaps
are
allowed
.

PASS



P
rogram to
A
lign
S
hort
S
equences



Performs gapped and ungapped alignment


onto a reference sequence



Seed words (11 and 12 bases)



Short reads (7 and 8 bases)



PST
-

calculated with the Needleman and


Wunsch

algorithm supplied with PASS



Handles data generated by
Solexa
,
SOLiD




or 454 technologies



Approach/Algorithm

Analysis and Results


Comparison of PASS with SOAP










PASS has better sensitivity with words of 11 and
runs at least 10 times faster

Save
money
-

Optimal pooling method


A set of experiments using the
Solexa

technology, based
on bacterial artificial chromosome (BAC) clones, and
address an experimental design problem.



Basic idea: More than one BAC per lane in order to
maximize the throughput of the
Solexa

technology, hence
minimize its cost.

Input strings (short reads)

Reference sequences

Inputs

Normal pooling method


One other hurdle in designing a globally optimal experiment is
the rapid proliferation of number of possible configurations. For
instance, if we would like to pool
m=150 BACs into 15 groups of
size=10, we would need to consider


Infeasible to search all
these configurations

Optimal Pooling method

Input strings (short reads)

Reference sequence

Optimal Pooling method

Input strings (short reads)

Reference sequences

Optimal Pooling method

Input strings (short reads)

Reference sequences

Optimal Pooling method

Pool

Problem


How to separate the groups of short reads?

Input strings (short reads)

Reference sequence

Optimal Pooling method

Pool

Two cases

Result

Conclusion


Program for Save time


“PASS
: a Program to Align Short Sequences

Davide

Campagna

et al
. Bioinformatics
(2009
)”



Algorithm for Save money


“Optimal
pooling for genome re
-
sequencing with ultra
-
high
-
throughput short
-
read
technologies,

Iman

Hajirasouliha
, Bioinformatics
(2008)



Q & A