GotohScan statistics

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Citations per year

Number of citations per year for the bioinformatics software tool GotohScan
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Tool usage distribution map

This map represents all the scientific publications referring to GotohScan per scientific context
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GotohScan specifications

Information


Unique identifier OMICS_18914
Name GotohScan
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
License GNU General Public License version 3.0
Computer skills Advanced
Version 1.3
Stability Stable
Source code URL http://www.bioinf.uni-leipzig.de/Software/GotohScan/GotohScan-1.3.tar.gz
Maintained Yes

Versioning


No version available

Documentation


Maintainer


  • person_outline Jana Hertel

Publication for GotohScan

GotohScan citations

 (7)
library_books

Differentiation of ncRNAs from small mRNAs in Escherichia coli O157:H7 EDL933 (EHEC) by combined RNAseq and RIBOseq – ryhB encodes the regulatory RNA RyhB and a peptide, RyhP

2017
BMC Genomics
PMCID: 5331693
PMID: 28245801
DOI: 10.1186/s12864-017-3586-9

[…] mined the functional enrichments returned for the predictions. CopraRNA was called with default parameters for each set of putative ncRNA homologs. To find ncRNA homologs for the CopraRNA prediction, GotohScan (v1.3 stable) [] was run with an e value threshold of 10−2 against the set of genomes listed in the Additional file : Table S2. The highest scoring homolog (i.e. having the lowest e value) f […]

library_books

Bioinformatics of prokaryotic RNAs

2014
RNA Biol
PMCID: 4152356
PMID: 24755880
DOI: 10.4161/rna.28647

[…] equence. Thus, it is not implicitly the method of choice. Specialized ncRNA sequence homology search derivates of blast are available, e.g., blastR. Semi-global dynamic programming algorithms such as Gotohscan are a viable alternative given the small genome size of prokaryotes. This program reports full-length hits, makes subsequent processing of the predicted homologs much easier, and is particul […]

library_books

Accessibility and conservation

2012
RNA Biol
PMCID: 3495738
PMID: 22767260
DOI: 10.4161/rna.20294

[…] of 21 enterobacterial species were retrieved from NCBI RefSeq database (see ; ). Homologs of each E. coli and Salmonella sRNA were identified in these 21 genomes using the semi-global alignment tool GotohScan (E-value cut-off of 0.01). Sequence-based alignment methods as GotohScan are appropriate for structural RNAs when the pairwise sequence identity is at least 50–60 percent. Therefore, to redu […]

library_books

Searching for Non coding RNAs in Genomic Sequences Using ncRNAscout

2012
PMCID: 5054157
PMID: 22768985
DOI: 10.1016/j.gpb.2012.05.004

[…] uitable for ncRNA searches. Infernal has been applied to roX1 RNA detection in Drosophila genomes . However, these tools are limited in the numbers of ncRNA families they are able to detect. The tool GotohScan attempts to fix these problems with homology search by utilizing a semi-global alignment approach. GotohScan performs fairly well compared to the aforementioned tools as it is able to ident […]

library_books

Evolution of the let 7 microRNA Family

2012
RNA Biol
PMCID: 3384580
PMID: 22617875
DOI: 10.4161/rna.18974

[…] to search the genomes of 60 deuterostomes in order to collect a comprehensive data set. In cases where BLAST was not able to detect a certain homolog, we used the semi-global sequence alignment tool GotohScan and finally Infernal.In order to firmly establish orthology relations, we determined for each microRNA gene its genomic context: for intergenic microRNAs, we recorded both adjacent protein-c […]

library_books

Local structural alignment of RNA with affine gap model

2011
BMC Proc
PMCID: 3090760
PMID: 21554760
DOI: 10.1186/1753-6561-5-S2-S2

[…] sequence similarity which may not work well for families in which members do not have high sequence similarity (e.g. members of RF00017 in Rfam 9.1 [] only have 39% sequence similarity). For example, Gotohscan [] considers semi-global alignment with affine gap penalty according to the sequence similarity only. For those also consider the similarity of secondary structure, they usually require the […]


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GotohScan institution(s)
Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany; Division of Ecology and Evolution, Institut fur Tierokologie und Zellbiologie, Tierarztliche Hochschule Hannover, Hannover, Germany; Department of Theoretical Chemistry, University of Vienna, Wien, Austria; Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA; RNomics Group, Fraunhofer Institut fur Zelltherapie und Immunologie, Leipzig, Germany; Santa Fe Institute, Santa Fe, NM, USA
GotohScan funding source(s)
Supported by Deutsche ForschungsGemeinschaft (through the ‘Graduierten-Kolleg Wissensreprasentation’ University of Leipzig); Austrian Fonds zur Forderung der Wissenschaftlichen Forschung (project P19411 ‘Genomdynamik’); sixth Framework Programme of the European Union (projects SYNLET and EMBIO); Alexander von Humboldt Foundation and John Templeton Foundations, and an Alexander von Humboldt Research Fellowship.

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