A Unifying Framework for Seed Sensitivity and Its Application to Subset Seeds

A unifying framework for seed sensitivity and its application to subset seeds

scientific article published on April 2006

AN OVERVIEW OF THE ALGORITHMIC SESSION OF MCCMB'05

Algorithms for path-constrained sequence alignment

article by Tamar Pinhas et al published January 2014 in Journal of Discrete Algorithms

Approximate String Matching Using a Bidirectional Index

Approximate string matching using a bidirectional index

Back-Translation for Discovering Distant Protein Homologies

Back-translation for discovering distant protein homologies in the presence of frameshift mutations

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CPM’s 20th Anniversary: A Statistical Retrospective

Combinatorial Search on Graphs Motivated by Bioinformatics Applications: A Brief Survey

Computing the Longest Unbordered Substring

Cross-Document Pattern Matching

Cross-document pattern matching

Decidability of Regularity and Related Properties of Ground Normal Form Languages

Designing Efficient Spaced Seeds for SOLiD Read Mapping

scientific article

Diversity and structure of PIF/Harbinger-like elements in the genome of Medicago truncatula

scientific article published on 9 November 2007

Diversity of monomers in nonribosomal peptides: towards the prediction of origin and biological activity.

scientific article

Editorial

Efficient alternatives to PSI-BLAST

Estimating seed sensitivity on homogeneous alignments

article

Evolution of biosequence search algorithms: a brief survey

scientific article published on 01 October 2019

Finding approximate repetitions under Hamming distance

article published in 2003

Finding repeats with fixed gap

Full-Fledged Real-Time Indexing for Constant Size Alphabets

Full-Fledged Real-Time Indexing for Constant Size Alphabets

Improved hit criteria for DNA local alignment

scientific article

Linear-time computation of local periods

Matching a set of strings with variable length don't cares

Minimal Absent Words in a Sliding Window and Applications to On-Line Pattern Matching

Minimal Discriminating Words Problem Revisited

Multiseed lossless filtration

scientific article published in January 2005

NORINE: a database of nonribosomal peptides

scientific article

On Maximal Unbordered Factors

On maximal repetitions of arbitrary exponent

On repetition-free binary words of minimal density

On subset seeds for protein alignment

scientific article published in July 2009

On the combinatorics of suffix arrays

scholarly article by Gregory Kucherov et al published November 2013 in Information Processing Letters

On-Line Construction of Position Heaps

On-line construction of position heaps

Optimal Bounds for Computing $$\alpha $$ α -gapped Repeats

Optimal neighborhood indexing for protein similarity search

scientific article

Pattern Matching on Sparse Suffix Trees

Prefix Table Construction and Conversion

article by Widmer Bland et al published 2013 in Lecture Notes in Computer Science

Protein Similarity Search with Subset Seeds on a Dedicated Reconfigurable Hardware

RNF: a general framework to evaluate NGS read mappers ⬇️

scientific article published on 9 September 2015

Rapid inference of antibiotic resistance and susceptibility by genomic neighbour typing

scientific article published on 10 February 2020

Reconsidering the significance of genomic word frequencies

scientific article published on 26 October 2007

Regular Language Constrained Sequence Alignment Revisited

article by Gregory Kucherov et al published 2011 in Lecture Notes in Computer Science

Regular language constrained sequence alignment revisited

scientific article published in May 2011

SIGffRid: a tool to search for sigma factor binding sites in bacterial genomes using comparative approach and biologically driven statistics

scientific article

Searching for Gapped Palindromes

Searching for gapped palindromes

article published in 2009

Seed Design Framework for Mapping SOLiD Reads

Spaced seeds improve k-mer-based metagenomic classification. ⬇️

scientific article published on 25 July 2015

Structural pattern matching of nonribosomal peptides.

scientific article

The complexity of some complementation problems

The complexity of testing ground reducibility for linear word rewriting systems with variables

Undecidability of ground reducibility for word rewriting systems with variables

Using Cascading Bloom Filters to Improve the Memory Usage for de Brujin Graphs

Using cascading Bloom filters to improve the memory usage for de Brujin graphs

scientific article published on 24 February 2014

Valentin Antimirov (1961–1995)

YASS: enhancing the sensitivity of DNA similarity search

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mreps: Efficient and flexible detection of tandem repeats in DNA

scientific article