Probalign protocols

Probalign specifications

Information


Unique identifier OMICS_00985
Name Probalign
Alternative name eProbalign
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes
Wikipedia https://en.wikipedia.org/wiki/Probalign

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Maintainer


  • person_outline Usman Roshan <>

Additional information


Standalone: http://probalign.njit.edu/standalone.html

Information


Unique identifier OMICS_00985
Name Probalign
Alternative name eProbalign
Interface Web user interface
Restrictions to use None
Input data Some unaligned protein or nucleic acid sequences.
Input format FASTA
Output format FASTA,PDF
Computer skills Basic
Stability Stable
Maintained Yes
Wikipedia https://en.wikipedia.org/wiki/Probalign

Maintainer


  • person_outline Usman Roshan <>

Additional information


Standalone: http://probalign.njit.edu/standalone.html

Publications for Probalign

Probalign IN pipelines

 (3)
2013
PMCID: 3832898
PMID: 24112713
DOI: 10.1186/1471-2164-14-697

[…] of 1.2. only single copy core genes were used (i.e. clusters containing paralogs were excluded). the nucleotide sequences corresponding to each set of homologous core genes were aligned using probalign [84]. alignment columns with a posterior probability <0.6 were removed, and alignments with >50% of the sites removed were discarded from the analysis. using each of the alignments […]

2011
PMCID: 3213126
PMID: 22102902
DOI: 10.1371/journal.pone.0027507

[…] ssu sequences were computed by clustalx [53], followed by manual refinement where necessary. because of the high number of indels, for the alignment of the its1 – 5.8s – its2 sequences we used the probalign algorithm [54] with default settings. leading and trailing gaps were deleted from the alignments. indels in the its alignment were recoded as a binary matrix by means of the simple indel […]

2008
PMCID: 2248559
PMID: 18226231
DOI: 10.1186/1471-2105-9-61

[…] both directions until the entire query, but not its flanks, is matched to the genomic sequence. this improves sequence coverage, reduces the false negative rate, and also allows a fair comparison to probalign and clustalw, both of which return global alignments of the entire sequences. for each method, we take the part of the genomic sequence aligned to the query in its alignment, and measure […]

Probalign institution(s)
Department of Computer Science, New Jersey Institute of Technology, University of North Carolina, Charlotte, NC, USA; Department of Computer Science and Bioinformatics Research Center, University of North Carolina, Charlotte, NC, USA
Probalign funding source(s)
Supported, in part, by NIH R01 GM073082-0181.

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