Literature DB >> 33584150

Yet Another Quick Assembly, Analysis and Trimming Tool (YAQAAT): A Server for the Automated Assembly and Analysis of Sanger Sequencing Data.

Darius Wen-Shuo Koh1, Kwok-Fong Chan2, Weiling Wu2, Samuel Ken-En Gan1,2.   

Abstract

Even with the ubiquity of Sanger sequencing, automated assembly software are predominantly stand-alone software packages for desktop/laptop use with very few online equivalents, thus geospatially constraining sequence analysis and assembly. With increased data output worldwide, there is also a need for automated quality checks and trimming prior to large assemblies, along with automated detection of mutations. Through web servers with expanded automation and functionalities, even smartphones/phablets can be used to perform complex analysis previously limited to desktops, especially if they can upload files from cloud storage. To facilitate such online accessible sequence assembly and analysis, we created Yet Another Quick Assembly, Analysis and Trimming Tool web server for the automated assembly of multiple .ab1 and .FASTQ sequencing reads de novo with automated trimming and scanning of the assembled sequences for single nucleotide polymorphisms and insertions or deletions without installation of software, allowing it to be accessed from anywhere with Internet access and with minimal dependency on other software and web tools. © Association of Biomolecular Resource Facilities.

Keywords:  AB1; FASTQ; INDEL; SNP; batch assembly

Year:  2021        PMID: 33584150      PMCID: PMC7861051          DOI: 10.7171/jbt.2021-3202-003

Source DB:  PubMed          Journal:  J Biomol Tech        ISSN: 1524-0215


  18 in total

1.  Adaptive seeds tame genomic sequence comparison.

Authors:  Szymon M Kiełbasa; Raymond Wan; Kengo Sato; Paul Horton; Martin C Frith
Journal:  Genome Res       Date:  2011-01-05       Impact factor: 9.043

2.  Directed Evolution of a Bright Near-Infrared Fluorescent Rhodopsin Using a Synthetic Chromophore.

Authors:  Lukas Herwig; Austin J Rice; Claire N Bedbrook; Ruijie K Zhang; Antti Lignell; Jackson K B Cahn; Hans Renata; Sheel C Dodani; Inha Cho; Long Cai; Viviana Gradinaru; Frances H Arnold
Journal:  Cell Chem Biol       Date:  2017-03-02       Impact factor: 8.116

3.  Mutations in HIV-1 reverse transcriptase affect the errors made in a single cycle of viral replication.

Authors:  Michael E Abram; Andrea L Ferris; Kalyan Das; Octavio Quinoñes; Wei Shao; Steven Tuske; W Gregory Alvord; Eddy Arnold; Stephen H Hughes
Journal:  J Virol       Date:  2014-04-23       Impact factor: 5.103

4.  Base-calling of automated sequencer traces using phred. II. Error probabilities.

Authors:  B Ewing; P Green
Journal:  Genome Res       Date:  1998-03       Impact factor: 9.043

5.  MAFFT multiple sequence alignment software version 7: improvements in performance and usability.

Authors:  Kazutaka Katoh; Daron M Standley
Journal:  Mol Biol Evol       Date:  2013-01-16       Impact factor: 16.240

6.  BLAST+: architecture and applications.

Authors:  Christiam Camacho; George Coulouris; Vahram Avagyan; Ning Ma; Jason Papadopoulos; Kevin Bealer; Thomas L Madden
Journal:  BMC Bioinformatics       Date:  2009-12-15       Impact factor: 3.169

7.  Biopython: freely available Python tools for computational molecular biology and bioinformatics.

Authors:  Peter J A Cock; Tiago Antao; Jeffrey T Chang; Brad A Chapman; Cymon J Cox; Andrew Dalke; Iddo Friedberg; Thomas Hamelryck; Frank Kauff; Bartek Wilczynski; Michiel J L de Hoon
Journal:  Bioinformatics       Date:  2009-03-20       Impact factor: 6.937

8.  Predicting sites of ADAR editing in double-stranded RNA.

Authors:  Julie M Eggington; Tom Greene; Brenda L Bass
Journal:  Nat Commun       Date:  2011       Impact factor: 14.919

9.  AutoSeqMan: batch assembly of contigs for Sanger sequences.

Authors:  Jie-Qiong Jin; Yan-Bo Sun
Journal:  Zool Res       Date:  2018-03-18

10.  Spontaneous Mutations in HIV-1 Gag, Protease, RT p66 in the First Replication Cycle and How They Appear: Insights from an In Vitro Assay on Mutation Rates and Types.

Authors:  Joshua Yi Yeo; Darius Wen-Shuo Koh; Ping Yap; Ghin-Ray Goh; Samuel Ken-En Gan
Journal:  Int J Mol Sci       Date:  2020-12-31       Impact factor: 5.923

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