sequence-to-function modeling

Simple adjustment of the sequence weight algorithm remarkably enhances PSI-BLAST performance

The paper improves PSI-BLAST performance by adjusting sequence weight calculation to avoid narrow blocks, showing significant gains in benchmark tests.

Progressive Multiple Sequence Alignment With The Poisson Indel Process

This paper introduces a progressive alignment method using a Poisson indel process model, achieving polynomial time complexity for multiple sequence alignment.

Deep Recurrent Neural Network for Protein Function Prediction from Sequence

Bidirectional LSTMs read raw amino-acid sequence to call protein function without alignment; ten unannotated iron-sequestration candidates flagged in UniRef100 lowered free iron when expressed in E. coli.

Co-estimation of Phylogeny-aware Alignment and Phylogenetic Tree

The paper introduces Canopy, a tool for parallelized alignment that reduces guide tree biases, showing it produces more accurate alignments than existing methods.

Genome-wide reconstruction of complex structural variants using read clouds

This paper introduces GROC-SVs, a method for detecting and assembling structural variants using read cloud data, showing improved specificity and enabling complex breakpoint reconstruction in cancer samples.

Qudaich: A smart sequence aligner

Qudaich is a sequence aligner designed for efficient pairwise comparisons of NGS datasets, offering faster and more useful alignments than existing tools.

RAFTS3: Rapid Alignment-Free Tool for Sequence Similarity Search

RAFTS3 is a fast alignment-free tool for protein sequence similarity search, outperforming BLASTp in speed with minimal sensitivity loss.

AptaTRACE: Elucidating Sequence-Structure Binding Motifs by Uncovering Selection Trends in HT-SELEX Experiments

AptaTRACE identifies sequence-structure binding motifs in HT-SELEX data by analyzing selection trends, improving efficiency in aptamer development.

FOCUS2: agile and sensitive classification of metagenomics data using a reduced database

FOCUS2 improves metagenomics sequence classification by being more sensitive, faster, and computationally efficient than existing methods.

Genome-wide characterization of PRE-1 reveals a hidden evolutionary relationship between suidae and primates

The paper characterizes a PRE-1 element in pigs, showing its structural and evolutionary similarities to primate Alu elements, suggesting a close evolutionary relationship between suidae and primates.

Haplotype-phased synthetic long reads from short-read sequencing

This paper introduces a method to generate long synthetic reads from short reads, achieving high accuracy across various genomic samples and applications.

Similarity Estimation Between DNA Sequences Based on Local Pattern Histograms of Binary Images

The paper introduces a method to estimate DNA sequence similarity using local pattern histograms from binary images, finding histogram intersection and Manhattan distance to be most effective.

SW#db: GPU-accelerated exact sequence similarity database search

The paper introduces SW#db, a GPU-accelerated tool for exact protein sequence similarity search, showing faster performance than existing methods on specific tasks.

Faster sequence alignment through GPU-accelerated restriction of the seed-and-extend search space

The paper introduces A21, a GPU-accelerated read aligner that improves speed and sensitivity by restricting the seed-and-extend search space using parallel sort and reduction techniques.

adabmDCA 2.0 - a flexible but easy-to-use package for Direct Coupling Analysis

adabmDCA 2.0 provides a flexible and multi-language implementation of Direct Coupling Analysis for protein and RNA sequence data, enabling tasks like contact prediction and sequence design.