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Protein sequence to structure alignment that includes secondary structure, structural conservation, structure-derived sequence profiles, and consensus alignment scores: Protein: Both: D. Chivian & D. Baker [23] 2003 LALIGN Multiple, non-overlapping, local similarity (same algorithm as SIM) Both: Local non-overlapping: W. Pearson: 1991 ...
A graph-based algorithm that constructs a graph of the sequence. no [11] SubSeqer: 2008 web: A graph-based approach for the detection and identification of repetitive elements in low–complexity sequences. no [12] ANNIE: 2009 web: This method creates an automation of the sequence analytic process. no [13] LPS-annotate 2011 on request
Also known as overlapping peptide scan or pepscan analysis, this technique uses a library of oligopeptide sequences from overlapping and non-overlapping segments of a target protein, and tests for their ability to bind the antibody of interest. This method is fast, relatively inexpensive, and specifically suited to profile epitopes for large ...
PANDASeq.is a program to align Illumina reads, optionally with PCR primers embedded in the sequence, and reconstruct an overlapping sequence. PEAR [ 41 ] PEAR: Illumina Paired-End reAd mergeR. qRNASeq script The qRNAseq tool can be used to accurately eliminate PCR duplicates from RNA-Seq data if Molecular Indexes™ or other stochastic labels ...
An overlapping gene (or OLG) [1] [2] is a gene whose expressible nucleotide sequence partially overlaps with the expressible nucleotide sequence of another gene. [3] In this way, a nucleotide sequence may make a contribution to the function of one or more gene products .
A reading frame is defined by the initial triplet of nucleotides from which translation starts. It sets the frame for a run of successive, non-overlapping codons, which is known as an "open reading frame" (ORF). For example, the string 5'-AAATGAACG-3' (see figure), if read from the first position, contains the codons AAA, TGA, and ACG ; if read ...
De novo sequence assemblers are a type of program that assembles short nucleotide sequences into longer ones without the use of a reference genome. These are most commonly used in bioinformatic studies to assemble genomes or transcriptomes. Two common types of de novo assemblers are greedy algorithm assemblers and De Bruijn graph assemblers.
Short read assemblers generally use one of two basic algorithms: overlap graphs and de Bruijn graphs. [10] Overlap graphs are utilized for most assemblers designed for Sanger sequenced reads. The overlaps between each pair of reads is computed and compiled into a graph, in which each node represents a single sequence read.
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