Two sequences Multiple sequences Local Blastz (zPicture-dcode.org) ALIGNMENTCONVERVED TFBS LAGAN...
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Transcript of Two sequences Multiple sequences Local Blastz (zPicture-dcode.org) ALIGNMENTCONVERVED TFBS LAGAN...
Two sequences
Multiple sequences
Loca
lLo
cal
Blastz(zPicture-dcode.org)
ALIGNMENT CONVERVED TFBS
LAGAN(mVISTA)
Global
Global
Global
Global
TBA/Multiz(Mulan-dcode.org)
LocalLocal
rVISTA at
at dcode.org
PROMOTER SEQUENCE ALIGNMENT
Promoter Sequence AlignmentDaniel Rico, PhD. [email protected] Rico, PhD. [email protected]
Whole Genome Alignments
• Local aligners– Work by “stacking” pairwise alignments– High specificity– BlastZ, LastZ, TBA + MultiZ
• Global aligners– Need to pre-define collinear segments– Better sensitivity– AVID/MAVID, LAGAN/MLAGAN, Pecan
• Mixed aligners– Combine both approaches– Shuffle-LAGAN, MAUVE
2
Reference Sequence Idea
– A sequence is fixed as the reference to which all other sequences are compared
S1: A T G C T CS2: A G A G CS3: T T C T GS4: A T T G C A T G C
S1: A T - G C - T - CS2: A - - G A - G - CS3: - T - T C - T - GS4: A T T G C A T G C
S1: A T G C T CS2: A - G A G C
S1: A T G C T CS2: A - G A G CS3: - T T C T G
3
S1: A T - G C - T - CS2: A - - G A - G - CS3: - T - T C - T - GS4: A T T G C A T G C
S1: A T G C T CS2: A G A G CS3: T T C T GS4: A T T G C A T G C
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BlastZ: Improved pairwise alignment of Genomic Sequences
Nucleotide local alignment program developed by Webb Miller's group (http://www.bx.psu.edu/miller_lab/)
BlastZ computes local alignments for sequences of any length based on the assumption that the input sequences are related and share blocks of high conservation that are separated by regions that lack homology and vary in length in the two sequences.
Penalizes gaps using a large gap-opening penalty and small gap-extension penalty, to reduce the over-penalization of longer gaps
Zpicture is web server for aligning 2 sequences wit BlastZ:
http://zpicture.dcode.org/5
AVID, LAGAN AND MLAGAN ASSUME THAT ONE HAS ALREADY
IDENTIFIED APPARENT ORTHOLOGOUS REGIONS BETWEEN TWO SPECIES, AND THAT THERE ARE
NO GENOMIC REARRANGEMENTS
7
Copyright OpenHelix.
VISTA Enhancer Browser
Enhancer Browser Combines computational and experimental data
Copyright OpenHelix.
VISTA Alignment display
104637349 GTAGTGCCACTGAGTGTGACAGGGATGGCAAGAAAAGCATTAAGTTCCAAGGGGAAAGAA 104637408>>>>>>>>> | || ||| ||| |||| |||||||||| | || || |||| | |||||||| <<<<<<<<<052290302 GAGATGTCACCAAGTA-AACAGAGATGGCAAGAGGACCAATAGGTTCTAGTGGGAAAGAC 052290360
“sliding window” to measure sequence conservation(default window size 100bp)
Graphical presentation of sequence conservation as “peaks-and-valley” curve
>70% identity
base sequence coordinates
%identity
(A) Standard stacked-pairwise visualization (smooth graph) of Mulan alignments of NOS-2 gene promoter. The human sequence (from -10 kb to +1 kb) was selected as the reference species. Repeats were masked in all species with RepeatMasker (Mulan settings); green regions in the base sequence indicate the human repeats. The graphical representations of the other sequences are displayed according to their similarity to the base sequence: the closer they are to human, the higher is the conservation (top sequences are less conserved). Parameters selected for detection of evolutionarily conserved regions (ECR) were 90 bp minimum length and minimum similarity of 65% (50% bottom cut-off). Red indicates regions that are upstream from the transcription start site; pink regions are downstream from it. Two conserved motifs in rodent NOS-2 promoters indicate the presence of distal and fragmented sequences that are very similar to the unique enhancer region conferring NF-κB regulation in human NOS-2. (B) A schematic representation of the hypothetical translocation of these sequences in human and rodents; double head arrows indicate the positional translocation.
Rico et al. BMC Genomics 2007 8:271 doi:10.1186/1471-2164-8-271
ECRs: Evolutionary Conserved Regions with Mulan
Promoter Sequence Alignment
Two sequences
Multiple sequences
Loca
lLo
cal
Blastz(zPicture-dcode.org)
ALIGNMENT CONVERVED TFBS
LAGAN(mVISTA)
Global
Global
Global
Global
TBA/Multiz(Mulan-dcode.org)
LocalLocal
rVISTA at
at dcode.org
PROMOTER SEQUENCE ALIGNMENT
Promoter Sequence AlignmentDaniel Rico, PhD. [email protected] Rico, PhD. [email protected]