PARALIGN statistics

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Citations per year

Number of citations per year for the bioinformatics software tool PARALIGN

Tool usage distribution map

This map represents all the scientific publications referring to PARALIGN per scientific context
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Associated diseases


Popular tool citations

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PARALIGN specifications


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


This tool is not available anymore.


Unique identifier OMICS_15917
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


No version available


This tool is not available anymore.

Publication for PARALIGN

PARALIGN citations


In Silico Design and Experimental Validation of siRNAs Targeting Conserved Regions of Multiple Hepatitis C Virus Genotypes

PLoS One
PMCID: 4956106
PMID: 27441640
DOI: 10.1371/journal.pone.0159211

[…] se, 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 comp […]


Coiled Coil Proteins Facilitated the Functional Expansion of the Centrosome

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

[…] were 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.) As an optimiz […]


Orthology prediction methods: A quality assessment using curated protein families

PMCID: 3193375
PMID: 21853451
DOI: 10.1002/bies.201100062

[…] DB, OrthoMCL, OMA): Due to the fast implementation and high scalability, there are many graph-based methods for multi-species comparisons. So far, all of them use either BLAST or Smith-Waterman (e.g. PARALIGN, SIMG) as sequence-similarity search algorithms. However, they are quite diverse regarding the clustering algorithms. COG, eggNOG, and OrthoDB share the same methodology: they identify three- […]


Correlating Traits of Gene Retention, Sequence Divergence, Duplicability and Essentiality in Vertebrates, Arthropods, and Fungi

Genome Biol Evol
PMCID: 3030422
PMID: 21148284
DOI: 10.1093/gbe/evq083

[…] 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 by their tria […]


Gene Expression in the Scleractinian Acropora microphthalma Exposed to High Solar Irradiance Reveals Elements of Photoprotection and Coral Bleaching

PLoS One
PMCID: 2980464
PMID: 21103042
DOI: 10.1371/journal.pone.0013975

[…] ition, longer sequences yield higher scores and lower e-values, which increase the chance of aligning significant matches.Smith-Waterman analysis of the 142 sequences used the high-performance Sencel Paralign application ( for local sequence alignments applied a calculated e-value of ≤10−2, equivalent to the value used successfully for the annotation of a complex marine micr […]


Structural insight into repair of alkylated DNA by a new superfamily of DNA glycosylases comprising HEAT like repeats

Nucleic Acids Res
PMCID: 1874660
PMID: 17395642
DOI: 10.1093/nar/gkm039

[…] numbers 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 homologs […]

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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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