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JAligner specifications

Information


Unique identifier OMICS_20021
Name JAligner
Software type Application/Script
Restrictions to use None
Programming languages Java
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes
Wikipedia https://en.wikipedia.org/wiki/JAligner

Information


Unique identifier OMICS_20021
Name JAligner
Software type Application/Script
Interface Command line interface, Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.0
Stability Stable
Maintained Yes
Wikipedia https://en.wikipedia.org/wiki/JAligner

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JAligner citations

 (8)
library_books

CATO: The Clone Alignment Tool

2016
PLoS One
PMCID: 4961376
PMID: 27459605
DOI: 10.1371/journal.pone.0159586

[…] scle [], and T-Coffee [] approaches. While both categories are applicable in this context, we elected to use the pair-wise Smith-Waterman algorithm with Gotoh’s affine gap penalty [] available in the JAligner package []. The gap penalties are configurable by the user and are set by default to 0.5. Pair-wise alignment algorithms facilitate an alignment of clone sequences against the standard refere […]

library_books

AluY mediated germline deletion, duplication and somatic stem cell reversion in UBE2T defines a new subtype of Fanconi anemia

2015
Hum Mol Genet
PMCID: 4550815
PMID: 26085575
DOI: 10.1093/hmg/ddv227

[…] breast cancer patients with an age at diagnosis <50 years, anonymized from the US clinical testing sample flow of Myriad Genetic Laboratories, using the Nextra Enrichment Kit (DC-121-1208, Illumina). JAligner was used for the initial mapping, followed by the variant calling, call quality assessment and review using in-house-developed software. The novel frameshift mutation in UBE2T, c.415_418insAG […]

library_books

Coiled Coil Proteins Facilitated the Functional Expansion of the Centrosome

2014
PLoS Comput Biol
PMCID: 4046923
PMID: 24901223
DOI: 10.1371/journal.pcbi.1003657

[…] ion that does not perform alignments, but only computes and returns the adjusted matrix (). For alignment, we use a modified Smith-Waterman-Gotoh algorithm , , based on the open-source implementation JAligner. In a Smith-Waterman alignment of two proteins, all possible pairs of residues are considered. In traditional algorithms, the same substitution matrix (e.g. BLOSUM62) is used for all pairs of […]

library_books

Analysis of the Cystic Fibrosis Lung Microbiota via Serial Illumina Sequencing of Bacterial 16S rRNA Hypervariable Regions

2012
PLoS One
PMCID: 3462755
PMID: 23056217
DOI: 10.1371/journal.pone.0045791

[…] Sequence reads were simulated using JAligner and in-house Java scripts as follows. Sequencing primers ( or published , , , ) were aligned to each taxon in the database (Bergey, Silva, or Greengenes) using JAligner with the EDNAFULL mat […]

library_books

A Novel Partial Sequence Alignment Tool for Finding Large Deletions

2012
Sci World J
PMCID: 3330604
PMID: 22566777
DOI: 10.1100/2012/694813

[…] en the sequences []. Next Generation sequencing (NGS) technology produces terabytes of sequencing data in an inexpensive way []. However, among these sequences, most NGS software such as Path, UGENE, JAligner, SSEARCH, Water, and others based on the well-known Smith-Waterman algorithm (SW) [–] is designed to align sequences with small gaps and may not be suitable when large deletions are present. […]

library_books

Reptilian transcriptome v1.0, a glimpse in the brain transcriptome of five divergent Sauropsida lineages and the phylogenetic position of turtles

2011
PMCID: 3192992
PMID: 21943375
DOI: 10.1186/2041-9139-2-19

[…] database consisted of nucleotide sequences, the orientation of each input sequence (forward or reverse complement) yielding the best alignment score against the database sequence was identified with JAligner [], whereas, for the protein databases, the input sequences were translated using the frame indicated by the best BLAST match. The query sequences were aligned against the database sequences […]

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