Project description
Advancing computational pangenomics via graph indexing
In the past, analysis of the human genome required a plethora of algorithmic tools which allowed for example the identification of genetic variations. However, using a single reference genome does not comply with the genetic variability of a population, and computational scientists are shifting towards pangenome graphs to represent variation. Pangenomes were originally proposed in the context of microbial analysis and describe commonly present and frequently absent genes and open reading frames in a population. The EU-funded REGINDEX project aims to advance the current knowledge of indexing data structures for graphs and extend the applicability of graph-based pangenome representations.
Objective
Sorting is, arguably, the most powerful algorithmic primitive when it comes to indexing data. At the same time, the regularities exposed by sorting are precisely those enabling data compression. In the last two decades, this fascinating duality has led researchers to the design of compressed full-text indexes: data structures supporting fast pattern matching queries over compressed text. In this project, we revisit the natural generalization of the problem to labeled graphs from a new perspective: we interpret graphs as finite-state automata and investigate the connections existing between their propensity to be sorted and the languages they recognize. Our novel language-theoretic approach makes it possible to transfer fundamental results between the mature fields of regular language theory and compressed text indexing. We aim at building this bridge by developing a new theory of compressed regular language indexing. This project finds fundamental applications to the rapidly-expanding field of computational pan-genomics, where the goal is to study the variations contained in the genomes of an entire population. Recent research has shown that representing pan-genomes as labeled graphs is an important step to reduce reference allele bias. Existing approaches, however, can index only restricted classes of graphs, thereby limiting the practical applicability of such powerful pan-genome representations. Our innovative approach, based on sorting regular languages by partial co-lexicographic orders, changes the perspective from which the compressed indexing problem has been tackled in the literature. This project aims at developing a theory of graph indexing and compression based on the natural interplay between sorting and regular language theory. We will apply these findings inside practical tools for aligning arbitrarily-long DNA fragments against compressed pan-genome graphs.
Fields of science (EuroSciVoc)
CORDIS classifies projects with EuroSciVoc, a multilingual taxonomy of fields of science, through a semi-automatic process based on NLP techniques. See: The European Science Vocabulary.
This project's classification has been human-validated.
CORDIS classifies projects with EuroSciVoc, a multilingual taxonomy of fields of science, through a semi-automatic process based on NLP techniques. See: The European Science Vocabulary.
This project's classification has been human-validated.
Keywords
Project’s keywords as indicated by the project coordinator. Not to be confused with the EuroSciVoc taxonomy (Fields of science)
Project’s keywords as indicated by the project coordinator. Not to be confused with the EuroSciVoc taxonomy (Fields of science)
Programme(s)
Multi-annual funding programmes that define the EU’s priorities for research and innovation.
Multi-annual funding programmes that define the EU’s priorities for research and innovation.
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HORIZON.1.1 - European Research Council (ERC)
MAIN PROGRAMME
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Topic(s)
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Calls for proposals are divided into topics. A topic defines a specific subject or area for which applicants can submit proposals. The description of a topic comprises its specific scope and the expected impact of the funded project.
Funding Scheme
Funding scheme (or “Type of Action”) inside a programme with common features. It specifies: the scope of what is funded; the reimbursement rate; specific evaluation criteria to qualify for funding; and the use of simplified forms of costs like lump sums.
Funding scheme (or “Type of Action”) inside a programme with common features. It specifies: the scope of what is funded; the reimbursement rate; specific evaluation criteria to qualify for funding; and the use of simplified forms of costs like lump sums.
HORIZON-ERC - HORIZON ERC Grants
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Call for proposal
Procedure for inviting applicants to submit project proposals, with the aim of receiving EU funding.
Procedure for inviting applicants to submit project proposals, with the aim of receiving EU funding.
(opens in new window) ERC-2021-STG
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Net EU financial contribution. The sum of money that the participant receives, deducted by the EU contribution to its linked third party. It considers the distribution of the EU financial contribution between direct beneficiaries of the project and other types of participants, like third-party participants.
30123 Venezia
Italy
The total costs incurred by this organisation to participate in the project, including direct and indirect costs. This amount is a subset of the overall project budget.