Alignment of Biological Sequences with Jalview.
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DOI: 10.1007/978-1-0716-1036-7_13
Abstract: In this chapter, we introduce core functionality of the Jalview interactive platform for the creation, analysis, and publication of multiple sequence alignments. A workflow is described based on Jalview's core functions: from data import to… read more here.
Keywords: alignment biological; biological sequences; biology; jalview ... See more keywords
A tool for feature extraction from biological sequences
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DOI: 10.1093/bib/bbac108
Abstract: With the advances in sequencing technologies, a huge amount of biological data is extracted nowadays. Analyzing this amount of data is beyond the ability of human beings, creating a splendid opportunity for machine learning methods… read more here.
Keywords: tool; biological sequences; feature extraction; sequences tool ... See more keywords
Aligning biological sequences by exploiting residue conservation and coevolution.
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DOI: 10.1103/physreve.102.062409
Abstract: Sequences of nucleotides (for DNA and RNA) or amino acids (for proteins) are central objects in biology. Among the most important computational problems is that of sequence alignment, i.e., arranging sequences from different organisms in… read more here.
Keywords: coevolution; aligning biological; biological sequences; conservation ... See more keywords
A new algorithm to train hidden Markov models for biological sequences with partial labels
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DOI: 10.1186/s12859-021-04080-0
Abstract: Background Hidden Markov models (HMM) are a powerful tool for analyzing biological sequences in a wide variety of applications, from profiling functional protein families to identifying functional domains. The standard method used for HMM training… read more here.
Keywords: hidden markov; method; algorithm train; biological sequences ... See more keywords
TreeCluster: Clustering biological sequences using phylogenetic trees
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DOI: 10.1371/journal.pone.0221068
Abstract: Clustering homologous sequences based on their similarity is a problem that appears in many bioinformatics applications. The fact that sequences cluster is ultimately the result of their phylogenetic relationships. Despite this observation and the natural… read more here.
Keywords: phylogenetic trees; using phylogenetic; biological sequences; sequences using ... See more keywords
SeqRepo: A system for managing local collections of biological sequences
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DOI: 10.1371/journal.pone.0239883
Abstract: Motivation Access to biological sequence data, such as genome, transcript, or protein sequence, is at the core of many bioinformatics analysis workflows. The National Center for Biotechnology Information (NCBI), Ensembl, and other sequence database maintainers… read more here.
Keywords: system; biological sequences; seqrepo; sequences seqrepo ... See more keywords
WalkIm: Compact image-based encoding for high-performance classification of biological sequences using simple tuning-free CNNs
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DOI: 10.1371/journal.pone.0267106
Abstract: The classification of biological sequences is an open issue for a variety of data sets, such as viral and metagenomics sequences. Therefore, many studies utilize neural network tools, as the well-known methods in this field,… read more here.
Keywords: classification biological; walkim; network; biological sequences ... See more keywords