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About 10,000 papers for “Multiple sequence alignment”

Multiple Sequence Alignment

Cecile Bester · Data Archiving and Networked Services (DANS) · 2023

Fasta files for Geneious multiple sequence alignments exported from Geneious Prime

Cited by 0Open access

Multiple sequence alignment

Sheila Lumley · Figshare · 2021

Multiple sequence alignment for manuscript describing how whole genome sequencing can be used to investigate nosocomial SARS-CoV-2 infection

Cited by 0Open access

Multiple sequence alignment.

Varsha Acharya (7381250), R. Arutselvan (13140875), Kalidas Pati (13140878) et al. · Figshare · 2022

<p>Multiple sequence alignment of YMBV_CP (coat protein) sequence with other CP viruses from the potyvirus family. The image is generated in Multalin software.</p> <p>(TIF)</p>

Cited by 0Open access

Multiple Sequence Alignment

Jin Xiong · Cambridge University Press eBooks · 2006

A natural extension of pairwise alignment is multiple sequence alignment, which is to align multiple related sequences to achieve optimal matching of the sequences. Related sequences are identified through the database similarity searching described in Chapter 4. As the process generates multiple matching sequence pairs, it is often necessary to convert the numerous pairwise alignments into a single alignment, which arranges sequences in such a way that evolutionarily equivalent positions across all sequences are matched.

Cited by 22

Multiple Sequence Alignment

Kazutaka Katoh · Methods in molecular biology · 2020

This volume discusses how to install and run tools for calculation and visualization of multiple sequence alignments (MSAs), and other analyses related to MSAs. Chapters cover basic and specially designed tools to deal with data resulting from recent developments in sequencing technologies.

Cited by 41Open access

Multiple sequence alignment.

Steven W. Adamson (489250), Rebecca E. Browning (489251), Khemraj Budachetri (489252) et al. · Figshare · 2015

<p>Multiple sequence alignment of the SEF amino acid sequence from <i>Amblyomma maculatum, Rhipicephalus pulchellus, Culex quinquefasciatus, Drosophila melanogaster</i>, and <i>Homo sapiens</i>.</p>

Cited by 0Open access

Multiple sequence alignment.

Iliano V. Coutinho-Abreu (359256), Narinder K. Sharma (359258), Maricela Robles-Murguia (359260) et al. · Figshare · 2015

<p>Multiple sequence alignment was performed with individual CBD domains identified from peritrophins from <i>P. papatasi</i> and <i>L. longipalpis</i>. Pp1CBD1, Pp1CBD2, Pp1CBD3, and Pp1CBD4 are PpPer1 CBDs. Pp2CBD1 is the single CBD in PpPer2. Pp3CBD1 and Pp3CBD2 are the two CBDs identified in PpPer3. Lulo1CBD1, Lulo1CBD2, Lulo1CBD3, and Lulo1CBD4 are the four CBDs in LuloPer1. Lulo2CBD1 and Lulo3CBD1 are the single CBDs in LuloPer2 and in LuloPer3, respectively. Ll3CBD1 and Ll3CBD2 are CBDs in LlPer3. Pp3put and Ll3put are putative domains similar to CBDs identified in <i>P. papatasi</i> PpPer3 and in <i>L. longipalpis</i> Ll3Per3. Such putative domain sequences also were identified in the N-terminal region of <i>C. felis</i> PL1 - CfPl1put; <i>C. quinquefasciatus</i> conserved hypothetical protein - Cq16put; and <i>A. aegypti</i> Ae51put, Ae45put, and Ae52put. The six conserved cysteines are highlighted in grey with the conserved aromatic amino acids predicted to bind chitin shown in white with black highlight; HRM motifs are underlined. Conserved amino acid residues displayed exclusively by the putative CBD domain sequences are shown in red, and the additional cysteine residues are indicated by asterisk (*).</p>

Cited by 0Open access

Multiple sequence alignment

Steven Prestwich, Des Higgins · 2000

Multiple sequence alignment is a central problem in Bioinformatics and a challenging one for optimisation algorithms. An established integer programming approach is to apply branch-and-cut to a graph-theoretical model. The models are exponentially large but are represented intensionally, and violated constraints can be located in polynomial time. This report describes a new integer program formulation that generates polynomial-sized models small enough to be passed to generic solvers. It is a hybrid formulation relating the sparse alignment graph with a compact encoding of the alignment matrix via channelling constraints. Alignments obtained with a pseudo-Boolean local search algorithm are competitive with those of state-of-the-art algorithms. Execution times are much longer, but in future work we aim to develop a more efficient specialised algorithm. 1

Cited by 0

Multiple sequence alignment.

Thomas J. Attard (13924790), Julie P. I. Welburn (13924793), Joseph A. Marsh (568755) · Figshare · 2022

<p>Multiple sequence alignment of all tubulin-α and β isotypes considered in this study.</p> <p>(PDF)</p>

Cited by 0Open access

Multiple Sequence Alignment

Tandy Warnow · Cambridge University Press eBooks · 2017

Phylogeny estimation generally begins by estimating a multiple sequence alignment on the set of sequences. Once the multiple sequence alignment is computed, a tree can then be computed on the alignment (Figure 9.1). Not surprisingly, errors in multiple sequence alignment estimation tend to produce errors in estimated trees (Ogden and Rosenberg, 2006; Nelesen et al., 2008; Liu et al., 2009a; Wang et al., 2012) and other downstream analyses. Hence, multiple sequence alignment is an important part of phylogeny estimation.

Cited by 1

Multiple sequence alignment.

Muhammad Sajid (710360), Saigha Marriam (12289600), Hamid Mukhtar (12289603) et al. · Figshare · 2022

Cited by 0Open access

Multiple sequence alignment.

Young-Sik Sohn (715070), Ho-Chul Shin (40398), Wei Sun Park (112223) et al. · Figshare · 2015

<p>Sequence homologues of Lpg0393 were identified by HHpred, and its non-redundant close relatives were aligned to a set of 10 distant Vps9 domains in the PF02204 of the Pfam database. Jalview was used for rendering. The secondary structure of Rabex-5 (PDB entry: 2OT3) and the predicted secondary structure of Lpg0393 are shown at the bottom of the alignment. Two key residues for the GEF activity of Rabex-5 and AtVps9a are coloured white on red. The aligned sequences are represented by a name of species. <i>Legionella shakespearei</i> (<i>Ls</i>; UPI000377E818), <i>Legionella longbeachae</i> (<i>Ll</i>; D3HLE8), <i>Legionella drancourtii</i> LLAP 12 (<i>Ld</i>; G9ET11), <i>Legionella tunisiensis</i> (<i>Lt</i>; UPI0002ECA82A), <i>Fluoribacter dumoffii</i> (<i>Fd</i>; UPI00026C7A1A), <i>Albugo laibachii</i> Nc14 (<i>Al</i>; F0WZN8), <i>Danio rerio</i> (<i>Dr</i>; F1QIZ1), <i>Entamoeba dispar</i> (<i>Ed</i>; entry code = B0EDB3), <i>Entamoeba histolytica</i> (<i>Eh</i>; C4LYL6), <i>Micromonas</i> sp. (<i>Ms</i>; C1E5E9), <i>Nematostella vectensis</i> (<i>Nv</i>; A7SBH6), and <i>Trichomonas vaginalis</i> (<i>Tv</i>; A2DH58).</p>

Cited by 0Open access

Multiple sequence alignment.

Francis O. Atanu (406749), Ernesto Oviedo-Orta (406750), Kimberly A. Watson (308014) · Figshare · 2015

<p>ClustalW alignment of the protein sequences of the major outer membrane protein (MOMP) from <i>C. pneumoniae</i> and members of the genus <i>Chlamydophila.</i> The solid boxes show the motifs putatively involved in substrate transport and selection. The pairwise percentage identity, to MOMP from <i>C. pneumoniae,</i> is indicated in parenthesis for each sequence. The dashed boxes show the four MOMP-derived peptides, as predicted using on-line epitope mapping prediction servers.</p>

Cited by 0Open access

Multiple sequence alignment.

Chuan Hong (322864), Hongen Jiang (306665), Enguo Lü (322865) et al. · Figshare · 2015

<p>Multiple sequence alignment of alpha S1 casein from bovine (Accession: ACG63494.1 GI: 195973860), goat (Accession: CAA51022.1 GI: 311943), sheep (Accession: ACJ46472.1 GI: 213391435), water buffalo (Accession: AAX49507.1 GI: 61658244) and horse (Accession: NP_001075352.1 GI: 126352302). The detected peptides by LC-MALDI-TOF-MS/MS are light grey. “*” identical residues, “:” conserved residues, and “.” semi-conserved residues.</p>

Cited by 0Open access

Multiple Sequence Alignment

Walter Pirovano, Jaap Heringa · Methods in molecular biology · 2008

Multiple sequence alignment (MSA) has assumed a key role in comparative structure and function analysis of biological sequences. It often leads to fundamental biological insight into sequence-structure-function relationships of nucleotide or protein sequence families. Significant advances have been achieved in this field, and many useful tools have been developed for constructing alignments. It should be stressed, however, that many complex biological and methodological issues are still open. This chapter first provides some background information and considerations associated with MSA techniques, concentrating on the alignment of protein sequences. Then, a practical overview of currently available methods and a description of their specific advantages and limitations are given, so that this chapter might constitute a helpful guide or starting point for researchers who aim to construct a reliable MSA.

Cited by 19