Services & Data
 
Services
GCAT | Panel
  The GCAT project aims to fill the existent gap in the development of haplotype panels by generating a dense haplotype map focused on the identification, characterization, and phasing of structural variants (SVs), the GCAT|Panel. In addition, we developed a comprehensive and detailed guide for the systematic inclusion of SVs in this type of study.
In this way, this resource will help improve the Genome-Wide Association Studies (GWAS) resolution, giving a step towards the inclusion of SVs into GWAS to start understanding the role of these variants in complex diseases. ( Jordi Valls-Margarit, Iván Galván-Femenía 2 , Daniel Matías-Sánchez, et. al. Nucleic Acids Res. 2022 ).
Guidance
  GUIDANCE is an integrated framework that is able to perform haplotype phasing, genotype imputation, association testing assuming different models of inheritance and phenome-wide association analysis (PheWAS) analysis of large GWAS datasets. Moreover, this application allows performing all these steps in a single execution, as well as in a modular way with optional user intervention. (M. Guindo-Martínez, R. Amela et al, Nat Commun. 2021).
SMuFin
  SMuFin (Somatic MUtation FINder) is a reference-free method designed to identify somatic variation on tumor genomes from the direct comparison with the corresponding normal genome of the same patient. Through a single execution SMuFin is able to identifying somatic single nucleotide variants (SNVs) and structural variants (SVs) of any size. (Moncunill V. & Gonzalez S., et al, Nature Biotechnology 2014).
ReLA
  ReLA (REgulatory region Local Alignment tool) is a method optimized with the Smith-Waterman algorithm that identifies gene regulatory regions in genomic DNA sequences through local searches of clusters of coincident transcription factor binding sites between two or more DNA sequences. ReLA can identify these regulatory regions through the comparison of homologous (orthologs and paralogs) or co-expressed sequences. Our server also allows the identification of more than one regulatory region (alternative promoters) within the reference sequence (Gonzalez S., et al, Bioinformatics 2012).