PARALIGN protocols

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PARALIGN specifications

Information


Unique identifier OMICS_15917
Name PARALIGN
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability No
Maintained No

Maintainer


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Information


Unique identifier OMICS_15917
Name PARALIGN
Software type Application/Script
Interface Command line interface
Restrictions to use Academic or non-commercial use
Operating system Unix/Linux, Mac OS
Computer skills Advanced
Stability No
Maintained No

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Publication for PARALIGN

PARALIGN in pipeline

2007
PMCID: 1874660
PMID: 17395642
DOI: 10.1093/nar/gkm039

[…] for the b. cereus alkc and alkd proteins are caj31884 and caj31885, respectively. single iteration sequence similarity searching in the ncbi non-redundant protein database were performed with paralign () and ncbi blast () and gave a set of approximately 80 significant hits (e-value <0.01) for b. cereus alkd. after removal of erroneous and redundant sequences, the remaining 43 alkd […]


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PARALIGN in publications

 (16)
PMCID: 4956106
PMID: 27441640
DOI: 10.1371/journal.pone.0159211

[…] near-complete matches to the human ncbi reference mrna sequence database [] were filtered out using the two database similarity-searching algorithms blast [] and smith-waterman, as implemented in paralign [,]. both algorithms were used to increase the validity percentage of our off-target search. the second phase of the off-target search was performed to filter out sirnas with seed-region […]

PMCID: 4046923
PMID: 24901223
DOI: 10.1371/journal.pcbi.1003657

[…] among top 50,000 hits or had a bitscore greater than 50., an all-against-all protein alignment was performed in multiple steps: first, a speed-optimized smith-waterman alignment was computed using paralign . hits from the first step were then re-aligned using the coiled-coil aware alignment algorithms. (for non-coiled-coil proteins, this step adds compositional matrix adjustment.) […]

PMCID: 3505970
PMID: 22965116
DOI: 10.1093/nar/gks839

[…] tremendous 15-fold upregulation (a). the refseq for 4933440m02rik is suppressed as no support for a protein encoded by this transcript has been found. parallel sequence alignment of 4933440m02rik in paralign 5.0 resulted in hits on 30 different mouse pirnas. an expanded search in pirnabank (http://pirnabank.ibab.ac.in) revealed a cluster of 225 individual pirnas containing the 4933440m02rik […]

PMCID: 3228760
PMID: 22144877
DOI: 10.1371/journal.pcbi.1002269

[…] outgroup genome (monosiga brevicollis) were assessed for completeness using the 1,126 single copy orthologs (see supplemental ). all the proteins from these draft genomes were aligned using the paralign software and the smith-waterman algorithm against the 363,805 proteins in eggnog. genome proteins were assigned to the menogs based on best reciprocal hits (with a bit score threshold […]

PMCID: 3030422
PMID: 21148284
DOI: 10.1093/gbe/evq083

[…] were retrieved from go., the classification of protein-coding genes into orthologous groups was based on a clustering procedure of all-against-all smith–waterman protein sequence comparisons using paralign () as implemented in the orthodb methodology (). the clustering procedure starts with the identification of all best reciprocal hits with an e value cutoff of 1 × 10−6, followed […]


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PARALIGN institution(s)
Centre for Molecular Biology and Neuroscience, Institute of Medical Microbiology, University of Oslo and Rikshospitalet-Radiumhospitalet HF, Oslo, Norway; Sencel Bioinformatics AS, Oslo, Norway; Department of Informatics, University of Oslo, Oslo, Norway
PARALIGN funding source(s)
This work was supported by the Research Council of Norway, in particular the National Programme for Research in Functional Genomics in Norway (FUGE), as well as the Norwegian Cancer Society.

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