BM-BC: A Bayesian Method of Base Calling for Solexa Sequence Data [PDF]
, 2012 Base calling is a critical step in the Solexa next-generation sequencing procedure. It compares the position-specific intensity measurements that reflect the signal strength of four possible bases (A, C, G, T) at each genomic position, and outputs ...
Jara, Alejandro +7 more
core +2 more sources
Sequence-dependent base pair stepping dynamics in XPD helicase unwinding
eLife, 2013 Helicases couple the chemical energy of ATP hydrolysis to directional translocation along nucleic acids and transient duplex separation. Understanding helicase mechanism requires that the basic physicochemical process of base pair separation be ...
Zhi Qi +3 more
doaj +1 more source
Application of Sequence Embedding in Protein Sequence-Based Predictions [PDF]
arXiv, 2021 In sequence-based predictions, conventionally an input sequence is represented by a multiple sequence alignment (MSA) or a representation derived from MSA, such as a position-specific scoring matrix. Recently, inspired by the development in natural language processing, several applications of sequence embedding have been observed.
arxiv
Base-By-Base Version 3: New Comparative Tools for Large Virus Genomes
Viruses, 2018 Base-By-Base is a comprehensive tool for the creation and editing of multiple sequence alignments that is coded in Java and runs on multiple platforms. It can be used with gene and protein sequences as well as with large viral genomes, which themselves ...
Shin-Lin Tu +5 more
doaj +1 more source
Kraken: ultrafast metagenomic sequence classification using exact alignments
Genome Biology, 2014 Kraken is an ultrafast and highly accurate program for assigning taxonomic labels to metagenomic DNA sequences. Previous programs designed for this task have been relatively slow and computationally expensive, forcing researchers to use faster abundance ...
Derrick E. Wood, S. Salzberg
semanticscholar +1 more source
A Gapless, Unambiguous Genome Sequence of the Enterohemorrhagic Escherichia coli O157:H7 Strain EDL933. [PDF]
, 2014 Escherichia coli EDL933 is the prototypic strain for enterohemorrhagic E. coli serotype O157:H7, associated with deadly food-borne outbreaks. Because the publicly available sequence of the EDL933 genome has gaps and >6,000 ambiguous base calls, we ...
Aziz, Ramy K +4 more
core +2 more sources
Peak Height Pattern in Dichloro-Rhodamine and Energy Transfer Dye Terminator Sequencing
BioTechniques, 1998 Establishing the pattern in peak heights within local sequence contexts improves the accuracy of base calling and the identification of DNA sequence variations in dye-terminator cycle sequencing.
H. Zakeri +4 more
doaj +1 more source
On a construction method of new moment sequences [PDF]
arXiv, 2023 In this paper we provide a way to construct new moment sequences from a given moment sequence. An operator based on multivariate positive polynomials is applied to get the new moment sequences. A class of new sequences is corresponding to a unique symmetric polynomial; if this polynomial is positive, then the new sequence becomes again a moment ...
arxiv
SleepEEGNet: Automated sleep stage scoring with sequence to sequence deep learning approach [PDF]
PLoS ONE, 2019 Electroencephalogram (EEG) is a common base signal used to monitor brain activities and diagnose sleep disorders. Manual sleep stage scoring is a time-consuming task for sleep experts and is limited by inter-rater reliability.
Sajad Mousavi, F. Afghah, U. R. Acharya
semanticscholar +1 more source
Mutational analysis of the gene start sequences of pneumonia virus of mice [PDF]
, 2007 The transcriptional start sequence of pneumonia virus of mice is more variable than that of the other pneumoviruses, with five different nine-base gene start (GS) sequences found in the PVM genome.
Dibben, Oliver +1 more
core +1 more source