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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

 (2)
library_books

Pareto optimization in algebraic dynamic programming

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

[…] 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 […]

library_books

Haploid to diploid alignment for variation calling assessment

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

[…] 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 […]


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

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