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The IPD and IMGT/HLA database: allele variant databases

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TLDR
The Immuno Polymorphism Database was developed to provide a centralized system for the study of polymorphism in genes of the immune system and continues to develop with new tools being added to address scientific developments, and to address user feedback and requests.
Abstract
The Immuno Polymorphism Database (IPD) was developed to provide a centralized system for the study of polymorphism in genes of the immune system. Through the IPD project we have established a central platform for the curation and publication of locus-specific databases involved either directly or related to the function of the Major Histocompatibility Complex in a number of different species. We have collaborated with specialist groups or nomenclature committees that curate the individual sections before they are submitted to IPD for online publication. IPD consists of five core databases, with the IMGT/HLA Database as the primary database. Through the work of the various nomenclature committees, the HLA Informatics Group and in collaboration with the European Bioinformatics Institute we are able to provide public access to this data through the website http://www.ebi.ac.uk/ipd/. The IPD project continues to develop with new tools being added to address scientific developments, such as Next Generation Sequencing, and to address user feedback and requests. Regular updates to the website ensure that new and confirmatory sequences are dispersed to the immunogenetics community, and the wider research and clinical communities.

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Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype

TL;DR: This work presents a method named HISAT2 (hierarchical indexing for spliced alignment of transcripts 2) that can align both DNA and RNA sequences using a graph Ferragina Manzini index, and uses it to represent and search an expanded model of the human reference genome.
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The EMBL-EBI search and sequence analysis tools APIs in 2019

TL;DR: The latest improvements made to the frameworks which enhance the interconnectivity between public EMBL-EBI resources and ultimately enhance biological data discoverability, accessibility, interoperability and reusability are described.
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IPD-IMGT/HLA Database.

TL;DR: The challenge for the IPD-IMGT/HLA Database is to continue to provide a highly curated database of sequence variants, while supporting the increased number of submissions and complexity of sequences.
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Tumor neoantigens: building a framework for personalized cancer immunotherapy

TL;DR: The identification of mutated and aberrantly expressed self-tumor antigens has been a time consuming and laborious task as mentioned in this paper, which has been solved by using next-generation sequencing and epitope prediction.
References
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TL;DR: A new approach to rapid sequence comparison, basic local alignment search tool (BLAST), directly approximates alignments that optimize a measure of local similarity, the maximal segment pair (MSP) score.
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Clustal w: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice

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TL;DR: Three computer programs for comparisons of protein and DNA sequences can be used to search sequence data bases, evaluate similarity scores, and identify periodic structures based on local sequence similarity.
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dbSNP: the NCBI database of genetic variation

TL;DR: The dbSNP database is a general catalog of genome variation to address the large-scale sampling designs required by association studies, gene mapping and evolutionary biology, and is integrated with other sources of information at NCBI such as GenBank, PubMed, LocusLink and the Human Genome Project data.
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