prettyplot protocols

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chevron_left Amino acid sequence alignment viewers Sequence alignment visualization chevron_right
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prettyplot specifications

Information


Unique identifier OMICS_16134
Name prettyplot
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data A sequence alignment.
Output data A sequence alignment image.
Operating system Unix/Linux, Mac OS, Windows
Programming languages C
License GNU General Public License version 3.0
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Ian Longden <>

prettyplot in pipeline

2010
PMCID: 2923621
PMID: 20805894
DOI: 10.1371/journal.pone.0012246

[…] trembl and interpro data banks were searched for sequences matching peptide p31-43 and p57-68 by using blast and fasta. sequence alignment was performed by using clustalw and visualized by prettyplot from the emboss suite., near-confluent caco2 cells in a 90-mm dish were incubated with egf and p31-43 at various times, after homogenization (10 mm tris-hcl [ph 7.4], 1 mm edta, […]


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prettyplot in publication

PMCID: 1780047
PMID: 17214893
DOI: 10.1186/1471-2164-8-15

[…] by analyzing why these seemingly non-functional proteins gave high scores in homology searches with hmmsearch. to analyze these cases at the genome level we used artemis [] and showorf, plotorf and prettyplot from the emboss package []. we found that in most cases a functional protein could be restored by an alternative gene start or frame-shift (17 cases), which we consider "restorable […]


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prettyplot institution(s)
Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK

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