EMBOSS: the European Molecular Biology Open Software Suite.

By Peter M. Rice, Ian Longden, A. Bleasby. 2000

9,437 citations recorded by the source corpus.

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In Molecular Biology

Citations in the corpus

CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats (2007, methodology): “Given a candidate consensus DR, the pattern search program fuzznuc of the EMBOSS package (28) is applied to get DRs’ positions in the related cluster.”
Biases in Illumina transcriptome sequencing caused by random hexamer priming (2010, background): “Pasteur Institute, which provides access to the EMBOSS (4) suite of programs.”
ProQ3: Improved model quality assessments using Rosetta energy terms (2016, methodology): “needle program from EMBOSS package [32] was used to align model and target sequences.”
TESTING FOR DIFFERENT RATES OF CONTINUOUS TRAIT EVOLUTION USING LIKELIHOOD (2006, methodology): “EMBOSS: the European molecular biology open software suite.”
Genetic Analysis of the Capsular Biosynthetic Locus from All 90 Pneumococcal Serotypes (2006, methodology): “Nucleotide differences were identified using the EMBOSS program Diffseq (MRC Rosalind Franklin Centre for Genomics Research, Hinxton, United Kingdom) [46].”
BIOINFORMATICS ORIGINAL PAPER (neutral): “…et al. , 2007), involving numerous interviews and a number end-user concerns that needed to be addressed: of data and results without the burden of unsafe copy-and-paste operations; (ii) management of scientiﬁc studies (e.g. retrieving parameters of a job, comparing results or user interface.”
QuickTree: building huge Neighbour-Joining trees of protein sequences (2002, methodology): “We have used the NEIGHBOR program as interfaced from the EMBOSS package (Rice et al., 2000), allowing us to perform analyses in batch mode.”
Genomic characterization of a novel SARS-CoV-2 (2020, methodology): “Then, differences in comparison with NC_045512 were extracted to create variants (Tables 1 & 2) (Rice et al., 2000).”
Repbase Update, a database of eukaryotic repetitive elements (2005, background): “They can virtually detect all possible arrays of tandem sequences and several independent programs were developed for this purpose, e.g. Tandem Repeat Finder (Benson, 1999); Satellites (Sagot and Myers, 1998); Etandem, Equicktandem (Rice et al., 2000); TROLL (Castelo et al., 2002).”
CleaveLand: a pipeline for using degradome data to find cleaved small RNA targets (2009, methodology): “All query sequences are aligned to each small RNA sequence using the Needle program in the EMBOSS package (Rice et al. , 2000).”
A Novel CpG Island Set Identifies Tissue-Specific Methylation at Developmental Gene Loci (2008, methodology): “Stacking energy and base twist were calculated using the EMBOSS b-twisted program with default settings[59].”