The Pipeline Repertoire for Ig-Seq Analysis

With the advent of high-throughput sequencing of immunoglobulin genes (Ig-Seq), the understanding of antibody repertoires and their dynamics among individuals and populations has become an exciting area of research. There is an increasing number of computational tools that aid in every step of the immune repertoire characterization. However, since not all tools function identically, every pipeline has its unique rationale and capabilities, creating a rich blend of useful features that may appear intimidating for newcomer laboratories with the desire to plunge into immune repertoire analysis to expand and improve their research; hence, all pipeline strengths and differences may not seem evident. In this review we provide a practical and organized list of the current set of computational tools, focusing on their most attractive features and differences in order to carry out the characterization of antibody repertoires so that the reader better decides a strategic approach for the experimental design, and computational pathways for the analyses of immune repertoires

Prediction of transcription factor bindings sites affected by SNPs located at the osteopontin promoter

This data contains information related to the research article entitled “Osteopontin splice variants and polymorphisms in Cancer Progression and Prognosis” [1]. Here, we describe an in silico analysis of transcription factors that could have altered binding to their DNA target sequence as a result of SNPs in the osteopontin gene promoter. We concentrated on SNPs associated with cancer risk and development. The analysis was performed with PROMO v3.0.2 software which incorporates TRANSFACT v6.4 of. We also present a figure depicting the putative transcription factor binding according to genotype

TDP-43 regulates its mRNA levels through a negative feedback loop

TAR DNA-binding protein-43 is a heterogeneous nuclear ribonucleoprotein involved in RNA metabolism, its aberrant localization and modification is also associated with a number of neurodegenerative diseases. Here, the TAR DNA-binding protein-43 protein negatively regulates its own mRNA levels, which may have consequences for pathogenesis