Calabrese2003

CREATED: 200904071016 LINK: url:~/Modules/Literature/Calabrese2003.pdf Title: Fast identification and statistical evaluation of segmental homologies in comparative maps

Segmental homologs: multiple pair of homologous features appear in roughly colinear order in two genomic segments

Advantages of FISH

• sensitive to clumps even when they account for only a small fraction of the
• feature homologies in the matrix
• does not strictly enforce colinearity
• fast
• can be integrated into automated analysis pipeline

Well-known examples of comparative maps include that of human and mouse (http://www.ncbi.nlm.nih.gov/Homology) and the major species of cereal grains (http://www.gramene.org).

Feature is typically a protein-coding gene but may be any entity to which it is possible to ascribe homology to other features.

Difficulties of highly divergenent SH include

• nucleotide substitutions obscure homology
• rearrangements subdivide one SH into multiple SH
• feature content diverges among homologous segments over tim due to gene loss
• and transposition
• minor rearrangement shuffle relative ordering and orientation of features
• individual genes appear to be duplicated at very high frequency

FISH

• for each entry $x$, define a neighborhood $T_x$, the only restruction on
• $T_x$ is that all entries are to the right of $x$.
• a k-clump is a set of points ${x_1, x_2, \ldots, x_k}$ such that $x_i = 1$
• and $x_{i+1} \in T_{x_i}$
• all maximal k-clumps can be found using dynamic programming
• a clump of size k or greater is a kg-clump, the probability distribution for
• number of kg-clumps can be approximated using the Chen_Stein Poisson
• approximation

Analysis of chromosomal duplications in Arabidopsis thaliana

• comparison of chromosome 2 and 4

Other computational approaches for identifying and evaluating SH

• [[Delcher1999]]
• [[Fujibichi2000]]
• [[Goldberg2000]]
• [[Gaut2001]]
• [[Vandepoele2002]]
• [[Durand2002]]