JAli statistics

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Citations per year

Number of citations per year for the bioinformatics software tool JAli
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Tool usage distribution map

This map represents all the scientific publications referring to JAli per scientific context
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JAli specifications

Information


Unique identifier OMICS_24726
Name JAli
Alternative name Jumping Alignments
Interface Web user interface
Restrictions to use None
Input data A protein sequence and a multiple alignment of a protein family.
Programming languages C
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Jens Stoye

Additional information


https://bibiserv.cebitec.uni-bielefeld.de/jali?id=jali_view_submission https://bibiserv.cebitec.uni-bielefeld.de/jali?id=jali_view_manual

Information


Unique identifier OMICS_24726
Name JAli
Alternative name Jumping Alignments
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input data A protein sequence and a multiple alignment of a protein family.
Operating system Unix/Linux, Mac OS, Windows
Programming languages C
Computer skills Advanced
Version 1.3
Stability Stable
Source code URL https://bibiserv.cebitec.uni-bielefeld.de/applications/jali/resources/downloads/jali-1.3.src.tar.gz
Maintained Yes

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Versioning


No version available

Maintainer


  • person_outline Jens Stoye

Additional information


https://bibiserv.cebitec.uni-bielefeld.de/jali?id=jali_view_submission https://bibiserv.cebitec.uni-bielefeld.de/jali?id=jali_view_manual

Publication for Jumping Alignments

JAli citations

 (5)
library_books

Pareto optimization in algebraic dynamic programming

2015
PMCID: 4491898
PMID: 26150892
DOI: 10.1186/s13015-015-0051-7

[…] Gotoh’s algorithm for sequence alignment under an affine gap model can be seen as an instance of this combination []. It minimizes the score sum of character matches, gap openings and gap extensions. Jumping alignments are another example []. They align a sequence to a multiple sequence alignment. The alignment always chooses the alignment row that fits best, but charges a cost for jumping to anot […]

library_books

Haploid to diploid alignment for variation calling assessment

2013
BMC Bioinformatics
PMCID: 3852041
PMID: 24564537
DOI: 10.1186/1471-2105-14-S15-S13

[…] A and any recombination B1 and B2 according to their alignment.The computation of such edit distance is an easy extension of the standard dynamic programming, and has been studied earlier under name jumping alignments in the context of amino acid sequences []. However, global alignment of full genomes is infeasible using standard quadratic time dynamic programming. Therefore we extend the diagona […]

library_books

TCRep 3D: An Automated In Silico Approach to Study the Structural Properties of TCR Repertoires

2011
PLoS One
PMCID: 3203878
PMID: 22053188
DOI: 10.1371/journal.pone.0026301

[…] ere performed by Modeller 9v5 software (http://salilab.org/modeller/modeller.html), loop modeling used the method of conjugated gradients combined with molecular dynamics and simulated annealing , . Jali performed single sequences alignments with structurally aligned block of crystal templates (http://bibiserv.techfak.uni-bielefeld.de/jali/). Potential hydrogen bonds were identified with the HBp […]

library_books

SAM: String based sequence search algorithm for mitochondrial DNA database queries

2011
PMCID: 3064999
PMID: 21056022
DOI: 10.1016/j.fsigen.2010.10.006

[…] plications that arise when novel length variation is encountered by following an operational approach . However, this strategy has never been fully adopted by the forensic community as it introduced “jumping alignments” that occasionally put haplotypes at further distances from each other than the actual mutations would suggest . Therefore, a phylogenetic approach to mtDNA sequence alignment has b […]

library_books

jpHMM at GOBICS: a web server to detect genomic recombinations in HIV 1

2006
Nucleic Acids Res
PMCID: 1538796
PMID: 16845050
DOI: 10.1093/nar/gkl255

[…] hich a classification into subclasses is available (). We called this method jumping profile Hidden Markov Model (jpHMM) since our approach is a probabilistic generalization of the jumping-alignment (JALI) algorithm proposed by Spang et al. (,). In JALI, a query sequence s is aligned to a multiple alignment A of a sequence family S = {s1, … , sn}—but s is not aligned to the alignment A as a whole, […]


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JAli institution(s)
Deutsches Krebsforschungszentrum (DKFZ), Theoretische Bioinformatik, Heidelberg, Germany

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