Sticky Hidden Markov Modeling of Comparative Genomic Hybridization

Comparative Genomic Hybridization (CGH)

Predicting CpG Islands and Their Relationship with Genomic Feature in Cattle by Hidden Markov Model Algorithm

Cattle supply an important source of nutrition for humans in the world. CpG islands (CGIs) are very important and useful, as they carry functionally relevant epigenetic loci for whole genome studies. As a matter of fact, there have been no formal analyses of CGIs at the DNA sequence level in cattle genomes and therefore this study was carried out to fill the gap. We used hidden markov model alg...

MAMOT: hidden Markov modeling tool

UNLABELLED Hidden Markov models (HMMs) are probabilistic models that are well adapted to many tasks in bioinformatics, for example, for predicting the occurrence of specific motifs in biological sequences. MAMOT is a command-line program for Unix-like operating systems, including MacOS X, that we developed to allow scientists to apply HMMs more easily in their research. One can define the archi...

Spectral Karyotyping and Comparative Genomic Hybridization Data

Spectral Karyotyping (SKY) (1–7) and Comparative Genomic Hybidization (CGH) (8– 11) are complementary fluorescent molecular cytogenetic techniques that have revolutionized the detection of chromosomal abnormalities. SKY permits the simultaneous visualization of all human or mouse chromosomes in a different color, facilitating the detection of chromosomal translocations and rearrangements (Figur...

Array comparative genomic hybridization in male infertility.

BACKGROUND Male infertility caused by a maturation arrest of spermatogenesis is a condition with an abrupt stop in spermatogenesis, mostly at the level of primary spermatocytes. The etiology remains largely unknown. METHODS We focused on patients with a complete arrest at the spermatocyte level (n = 9) and used array comparative genomic hybridization to screen for deletions or duplications th...