deepBlockAlign specifications

Information


Unique identifier OMICS_07347
Name deepBlockAlign
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Version 1.3.1
Stability Stable
Maintained Yes

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Publication for deepBlockAlign

deepBlockAlign in publications

 (3)
PMCID: 4437211
PMID: 26042150
DOI: 10.3389/fgene.2015.00188

[…] on the pattern by which the short reads map to a certain genomic region (read profile; figures , ) (pundhir and gorodkin, ). specifically, it utilizes a “read profile based alignment” algorithm, deepblockalign (langenberger et al., ) to compare read profiles from a candidate region with a database of known mirna read profiles, compiled using mirbase (kozomara and griffiths-jones, ). […]

PMCID: 4306309
PMID: 25674563
DOI: 10.3389/fbioe.2015.00007

[…] tools that have a graphic user interface (as opposed to being operated from the command line). tools that are run on a webserver (as opposed to being installed and run on a local machine)., deepblockalign is innovative in that it provides advanced scoring of the read signature, but does not evaluate the rna structure (langenberger et al., ; pundhir and gorodkin, ). deepblockalign uses […]

PMCID: 4124155
PMID: 24917120
DOI: 10.1186/1471-2164-15-459

[…] spaced (<30 nt) set of mapped reads were grouped into distinct so-called block groups using blockbuster [] and the resulting block group structures were compared by their read profiles using deepblockalign [] to obtain putative rna annotations of the unknown transcripts. see methods section for details., from blockbuster we found 1,127 block groups with a length of at least 50 nt, […]


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deepBlockAlign institution(s)
Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, Universität Leipzig, Leipzig, Germany

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