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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

 (8)
library_books

A comprehensive comparison of general RNA–RNA interaction prediction methods

2015
PMCID: 4838349
PMID: 26673718
DOI: 10.1093/nar/gkv1477

[…] sequence alignments (msa) of homologues., for the srna database, we obtained the list of 244 completed enterobacteriaceae genomes from kegg () and complete genomes listed from refseq. we used gotohscan () to find homologs for input reference sequences, and generated fasta files of unaligned hits from the output. fasta files were then aligned with mafft () in structurally-aware q-ins-i […]

library_books

Bioinformatics of prokaryotic RNAs

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

[…] 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, […]

library_books

Accessibility and conservation

2012
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, […]

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

[…] 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 […]

library_books

Evolution of the let 7 microRNA Family

2012
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 […]

library_books

Conservation and Occurrence of Trans Encoded sRNAs in the Rhizobiales

2011
PMCID: 3927594
PMID: 24710299
DOI: 10.3390/genes2040925

[…] structure, and uses this model to search all rhizobiales for further homologs., in the first stage of the workflow, putative homologs are obtained by sequence homology searches using blastn [] and gotohscan []. we initialize the search for homologous rna sequences of a reference sequence smelxnnn by employing blastn with e < 10−5 on the complete set of alphaproteobacterial genomes (for […]


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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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