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Parasail specifications

Information


Unique identifier OMICS_17883
Name Parasail
Alternative name Pairwise Sequence Alignment Library
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages C, Python
License Academic Free License version 3.0
Computer skills Advanced
Version 1.2
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Jeff Daily

Publication for Pairwise Sequence Alignment Library

Parasail citations

 (4)
library_books

Diversification of Secondary Metabolite Biosynthetic Gene Clusters Coincides with Lineage Divergence in Streptomyces

2018
PMCID: 5872123
PMID: 29438308
DOI: 10.3390/antibiotics7010012

[…] ASH 3.0 []. We also used an annotation-independent approach to identify SMGCs shared between genomes. For each SMGC identified by antiSMASH, we used Prodigal [] to call open reading frames (ORFs) and Parasail with default parameters to identify orthologous genes and orthologous gene groups []. We used the R package igraph [] to cluster similar SMGCs, define cluster membership, and thus determine w […]

library_books

xenoGI: reconstructing the history of genomic island insertions in clades of closely related bacteria

2018
BMC Bioinformatics
PMCID: 5799925
PMID: 29402213
DOI: 10.1186/s12859-018-2038-0

[…] nt BLAST hits, there will be nothing lower than this). b is a ceiling value for the alignment score (the score of the shorter sequence aligned against itself).The global alignment is calculated using Parasail []. The use of global alignment here reflects the fact that we are operating in a clade of closely related strains and the gene families we build consist of closely related genes. Because of […]

library_books

Quantification of Inter Sample Differences in T Cell Receptor Repertoires Using Sequence Based Information

2017
Front Immunol
PMCID: 5694755
PMID: 29187849
DOI: 10.3389/fimmu.2017.01500

[…] his is one of the SW algorithm using a single-instruction-multiple-data (SIMD) system, which allows for multiple units to simultaneously execute the same operation. The algorithm was implemented with Parasail, an open-source software for sequence alignment ().The SW algorithm requires amino acid substitution matrices, which determine the cost of the replacement of a single amino acid residue by an […]

library_books

Edlib: a C/C ++ library for fast, exact sequence alignment using edit distance

2017
Bioinformatics
PMCID: 5408825
PMID: 28453688
DOI: 10.1093/bioinformatics/btw753

[…] asail does not support infix and prefix semi-global methods. Regarding the alignment path, SeqAn could not complete our tests with semi-global methods because it was allocating too much memory, while Parasail and Myers do not support the finding of alignment path.As can be seen from the results, Edlib exhibits significant improvement in speed with increase of sequence similarity, in contrast to ot […]

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Parasail institution(s)
Pacific Northwest National Laboratory, High Performance Computing Group, Richland, WA, USA
Parasail funding source(s)
This work was supported by Pacific Northwest National Laboratory (PNNL) Institutional Overhead funds.

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