International audienceThis paper presents a seed-based algorithm for intensive DNA sequence comparison. The novelty comes from the way seeds are used to efficiently generate small ungapped alignments -- or HSPs (High Scoring Pairs) - in the first stage of the search. W-nt words are first indexed and all the 4^W possible seeds are enumerated following a strict order ensuring fast generation of unique HSPs. A prototype - written in C - has been realized and tested on large DNA banks. Speed-up compared to BLASTN range from 5 to 28 with comparable sensitivity
Summary: Multiple spaced seeds represent the current state-of-the-art for similarity search in bioin...
The main way of analyzing biological sequences is by comparing and aligning them to each other. It r...
The main way of analyzing biological sequences is by comparing and aligning them to each other. It r...
International audienceThis paper presents a seed-based algorithm for intensive DNA sequence comparis...
International audienceThis paper presents a seed-based algorithm for intensive DNA sequence comparis...
International audienceSequence similarity search is a common and repeated task in molecular biology....
International audienceSequence similarity search is a common and repeated task in molecular biology....
AbstractLarge-scale comparison of genomic DNA is of fundamental importance in annotating functional ...
International audienceThis paper presents a parallel architecture for computing genomic sequence ali...
International audienceThis paper presents a parallel architecture for computing genomic sequence ali...
The challenge of similarity search in massive DNA sequence databases has inspired major changes in B...
Large-scale comparison of genomic DNA is of fundamental importance in annotating functional elements...
Abstract Background The most frequently used tools in bioinformatics are those searching for similar...
Homology search finds similar segments between two biological sequences, such as DNA or protein sequ...
The main way of analyzing biological sequences is by comparing and aligning them to each other. It r...
Summary: Multiple spaced seeds represent the current state-of-the-art for similarity search in bioin...
The main way of analyzing biological sequences is by comparing and aligning them to each other. It r...
The main way of analyzing biological sequences is by comparing and aligning them to each other. It r...
International audienceThis paper presents a seed-based algorithm for intensive DNA sequence comparis...
International audienceThis paper presents a seed-based algorithm for intensive DNA sequence comparis...
International audienceSequence similarity search is a common and repeated task in molecular biology....
International audienceSequence similarity search is a common and repeated task in molecular biology....
AbstractLarge-scale comparison of genomic DNA is of fundamental importance in annotating functional ...
International audienceThis paper presents a parallel architecture for computing genomic sequence ali...
International audienceThis paper presents a parallel architecture for computing genomic sequence ali...
The challenge of similarity search in massive DNA sequence databases has inspired major changes in B...
Large-scale comparison of genomic DNA is of fundamental importance in annotating functional elements...
Abstract Background The most frequently used tools in bioinformatics are those searching for similar...
Homology search finds similar segments between two biological sequences, such as DNA or protein sequ...
The main way of analyzing biological sequences is by comparing and aligning them to each other. It r...
Summary: Multiple spaced seeds represent the current state-of-the-art for similarity search in bioin...
The main way of analyzing biological sequences is by comparing and aligning them to each other. It r...
The main way of analyzing biological sequences is by comparing and aligning them to each other. It r...