fish fast identification of segmental homology
DESCRIPTION
FISH Fast Identification of Segmental Homology. University of North Carolina at Chapel Hill. Shian-Gro Wu. Department of Computer Science and Information Engineering, National Taiwan University. Outline. Introduction Input data How it works From markers to features Form features to grid - PowerPoint PPT PresentationTRANSCRIPT
FISHFISHFast Identification of Segmental HomologyFast Identification of Segmental Homology
University of North Carolina at Chapel University of North Carolina at Chapel HillHill
Department of Computer Science and Department of Computer Science and Information Engineering, National Taiwan Information Engineering, National Taiwan UniversityUniversity
Shian-Gro WuShian-Gro Wu
OutlineOutline• IntroductionIntroduction• Input dataInput data• How it worksHow it works
– From markers to featuresFrom markers to features– Form features to gridForm features to grid– Form grid to bolcksForm grid to bolcks
IntroductionIntroduction
• FISH is software for the fast identification and statistical evaluation of segmental homologs.
genome
contig gene(marker)
IntroductionIntroduction
contigA
markers
contigB
contigA
features
contigB
contigA
contigB
points
contigA
contigB
blocks
Input dataInput data
• Each map file lists the names and transcriptional orientation (if known) of all the markers on one contig.
• Example <map1> gene names transcriptional orientation
At1g01010 1At1g01020 -1At1g01030 -1At1g01040 1At1g01050 -1...
marker
Input dataInput data
• Each match file lists all the homologies between markers in a pair of contigs.
• Example <match1v1>
gene names gene names match score At1g01010 At1g02240 94
At1g01010 At1g02250 91At1g01010 At1g32870 66At1g01010 At1g33060 43At1g01010 At1g52880 42....
From markers to From markers to featuresfeatures
contigA
markers
contigB
contigA
features
contigB
contigA
contigB
points
contigA
contigB
blocks
From markers to From markers to featuresfeatures
• step1step1– positions and transcriptional orientations
(when known) of the markers are read from a set of map files, one map file per contig. Markers within each map file must be ordered according to their physical positions on the contig.
– Individual homologies between markers are read from a set of match files. There is at least one, and no more than two, such files for each pair of contigs.A,B,CA,B,C A&A,A&B,A&C,B&A,B&B………A&A,A&B,A&C,B&A,B&B………
From markers to From markers to featuresfeatures
• step2step2– FISH performs detandemization, in
which multiple markers may be collapsed into single features.
– MIN Score and MAX Dist.
markers
features
a b c d e f g h
A B (B) C D (C) E F
From markers to featuresFrom markers to features1.ScoreAB > MIN Score
markA markB
ScoreAB
2.ScoreAC > MIN Score and ScoreBC > MIN Score
markA markB
ScoreAB
markA markB
ScoreAC
markC
ScoreBC
markA markB
ScoreABMAX Dist Range
Form features to gridForm features to grid
contigA
markers
contigB
contigA
features
contigB
contigA
contigB
points
contigA
contigB
blocks
Form features to gridForm features to grid
• In order to identify segmental homologies, FISH computes a grid for each pair of contigs.
• Points in the grid represent matches between pairs of features.
contigA
contigB
fA1 fA2 fA3 fA4
fB1 fB2 fB3 fB4
PointA1B2 PointB2A4
Form features to gridForm features to grid
• Each position in the grid, whether or not a point is present, is called as a cell.
cell (contigA,contigB) = feature (contigA) * feature (contigB)
cell (contigC,contigC) = feature (contigC) * [feature (contigC) -1] / 2
A
B
C
C
Form features to gridForm features to grid• contig markers features 1 6494 5913 2 4038 3711 3 5221 4777 • contig1 contig2 points cells 1 1 2143 17478828 1 2 2018 21943144 1 3 2088 28246400 2 2 751 6883905
….
Form features to Form features to gridgrid
contigA
markers
contigB
contigA
features
contigB
contigA
contigB
points
contigA
contigB
blocks
Form grid to bolcksForm grid to bolcks
• Defining the neighborhood size– FISH measures distance between
two points (Xi,Yi) and (Xj,Yj) using the Manhattan distance
– In order to be considered neighbors, two points must be closer than
jiji YYXXd
)1log(
)1log(
4
3
nm
TdT
m:number of points n:number of cells
Form grid to bolcksForm grid to bolcks
)1log(
)1log(
4
3
nm
TdT
m:number of pointsn:number of cells
If T=0.05
dT
m/n0.05
0.75
0.0001
23
ResultResult
Form grid to bolcksForm grid to bolcks
• Choosing among multiple neighborsChoosing among multiple neighbors– It can happen that a point may be in the
neighborhood of more than one other point. – FISH ranks the cells within each
neighborhood and chooses that neighbor having the highest rank
n
c
c
d
dwr
1)/1(
/1
Where n is the number of cells in the point’s neighborhood, dc is the distance of the cell from the point under consideration and w is the weight.
Reference
• User’s Manual for Fast Identification of Segmental Homology
http://www.bio.unc.edu/faculty/vision/lab/http://www.bio.unc.edu/faculty/vision/lab/FISH/FISH/
• Fast identification and statistical evaluation of segmental homologies in comparative maps
http://bioinformatics.oxfordjournals.org/cgi/http://bioinformatics.oxfordjournals.org/cgi/content/abstract/19/suppl_1/i74content/abstract/19/suppl_1/i74
Thank You