While solving biological problems, one encounters multiple types of genomic data or sometimes an aggregate of same type of data across multiple studies and decoding such huge amount of data manually is unfeasible and tedious. Therefore, integrated analysis of genomic data using statistical methods has become popular. The rapid advancement in high throughput technologies allows researchers to answer more complex biological questions enabling the development of statistical methods in integrated genomics to establish more effective therapeutic strategies for human disease. While studying the genome, there are some crucial aspects that should be taken in consideration. Gene prediction is the identification of genetic elements in a genomic sequence. This study is based on a combination of approaches: de novo, homology prediction, and transcription. Tools such as EvidenceModeler are used to merge the different results. Gene structure also have been compared, including mRNA length, exon length, intron length, exon number, and non-coding RNA. Analysis of repeated sequences has been found useful in reconstructing species divergence timelines. In order to preserve a specie, knowledge of the mating system is crucial: scientists can stabilize wild populations through captive breeding, followed by the release in the environment of new individuals. This task is particularly difficult by considering the species with homomorphic sex chromosomes and a large genome. For example, in the case of amphibians, there are multiple transitions among male and/or female heterogamety. Sometimes even variation of sex chromosomes within amphibian populations of the same specie were reported. The multiple transitions among XY and ZW systems that occur in amphibians determine the sex chromosome systems to be labile in salamanders populations. By understanding the chromosomal basis of sex of those species, it is possible to reconstruct the phylogenetic history of those families and use more efficient strategies in their conservation. By using the ddRADseq method scientists find new sex-related loci in a 56 Gb genome of "Cryptobranchidae" family. Their results support the hypothesis of female heterogamety of this species. These loci were confirmed through the bioinformatic analysis of presence/absence of that genetic locus in sex-knowing individuals. Their sex was determined previously by ultrasound, laparoscopy and by measuring serum calcium level differences. The determination of those candidate sexual loci was performed considering valid both the female-heterogametic and the male-heterogametic. Finally to evaluate the validity of those loci, they were amplified through PCR directly from samples of known-sex individuals. This final step led to the demonstration of female-heterogametic of several divergent populations of "Cryptobranchidae" family.