Protocols

MALIGN specifications

Information


Unique identifier OMICS_26320
Name MALIGN
Software type Application/Script
Interface Command line interface, Graphical user interface
Restrictions to use None
Input data A nucleic acids file and an amino acid sequences file.
Input format GenBank
Operating system Unix/Linux, Mac OS, Windows
License GNU General Public License version 3.0
Computer skills Advanced
Version 2.7
Stability Stable
Source code URL https://www.amnh.org/content/download/61087/1019190/version/1/file/malign.tar.gz
Maintained No

Versioning


No version available

Documentation


Maintainer


This tool is not maintained anymore.

Publication for MALIGN

MALIGN citations

 (2)
call_split

SNP Discovery with EST and NextGen Sequencing in Switchgrass (Panicum virgatum L.)

2012
PLoS One
PMCID: 3458043
PMID: 23049744
DOI: 10.1371/journal.pone.0044112
call_split See protocol

[…] esirable sequences such as those matching non-cellular and rRNA sequences. Once identified, those sequences were removed from the final set of processed ESTs. For clustering, ESTs were evaluated with malign, a k-mer-based alignment tool , which clusters ESTs based on sequence overlap (k-mer  = 16, seed length requirement  = 32, alignment identity > = 98%). Clusters of ESTs were further merged base […]

call_split

Analyses of expressed sequence tags from the maize foliar pathogen Cercospora zeae maydis identify novel genes expressed during vegetative, infectious, and reproductive growth

2008
BMC Genomics
PMCID: 2596140
PMID: 18983654
DOI: 10.1186/1471-2164-9-523
call_split See protocol

[…] ared against the GenBank nucleotide database by BLAST [] to identify contaminants; undesirable ESTs such as those matching non-cellular sequences were removed.For clustering, ESTs were evaluated with MALIGN [], a kmer-based alignment tool that clusters ESTs based on sequence overlap (kmer = 16, seed length requirement = 32, alignment ID >= 98%). Clusters of ESTs were further merged based on sister […]

MALIGN institution(s)
Department of Invertebrates, American Museum of Natural History, New York, NY, USA

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