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Unique identifier OMICS_00998
Name SWIPE
Alternative name Smith-Waterman database searches with inter-sequence SIMD parallelisation
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Documentation


Publication for Smith-Waterman database searches with inter-sequence SIMD parallelisation

SWIPE citations

 (8)
library_books

Know Your Enemy: Successful Bioinformatic Approaches to Predict Functional RNA Structures in Viral RNAs

2018
Front Microbiol
PMCID: 5758548
PMID: 29354101
DOI: 10.3389/fmicb.2017.02582

[…] test sensitivity available: 7. Alternatively, more sensitive local similarity search programs based on Smith-Waterman algorithm such as FASTA (SSEARCH; Lipman and Pearson, ; Pearson and Lipman, ) and SWIPE (Rognes, ) may be used, but are slower than blastn. FASTA is available through EMBL-EBI tools (https://www.ebi.ac.uk/Tools; Mcwilliam et al., ). Creating alignments for detection of elements wit […]

library_books

Computing Platforms for Big Biological Data Analytics: Perspectives and Challenges

2017
Comput Struct Biotechnol J
PMCID: 5581845
PMID: 28883909
DOI: 10.1016/j.csbj.2017.07.004

[…] not fully filled at startup and finishing stages. A pretty-fast SSE2 approach proposed by Farrar in 2007  uses a striped strategy to overcome the dependency along the query sequence. Rognes proposed SWIPE  in 2011, which is considered as the fastest SSE implementation. Unlike previous approaches, SWIPE takes inter-sequence parallelism and the score profile strategy for efficient score fetching. T […]

call_split

Heterogeneous molecular processes among the causes of how sequence similarity scores can fail to recapitulate phylogeny

2016
Brief Bioinform
PMCID: 5429007
PMID: 27103098
DOI: 10.1093/bib/bbw034
call_split See protocol

[…] rams are heuristic and so the alignments are not guaranteed to be the best possible hits. Therefore, pairwise alignments were also conducted using the exact Smith-Waterman algorithm as implemented in SWIPE []. The parameters used for blastn and blastp included an E-value cutoff of E≤10−10 and word sizes of four for blastn and three for blastp. The state space of amino acids and nucleotides differs […]

library_books

Functional Responses of Salt Marsh Microbial Communities to Long Term Nutrient Enrichment

2016
Appl Environ Microbiol
PMCID: 4836423
PMID: 26944843
DOI: 10.1128/AEM.03990-15

[…] 169 typical nosZ sequences and 70 atypical sequences. Metagenomic reads were then queried against this database, with all six reading frame translations of each read using tblastn implemented in the SWIPE aligner () and with a bit score threshold of 80.Some of our metagenomic reads had multiple matches to both typical and atypical sequences in the nosZ reference set, with a bit score greater than […]

library_books

Lineage specific gene radiations underlie the evolution of novel betalain pigmentation in Caryophyllales

2015
New Phytol
PMCID: 4557044
PMID: 25966996
DOI: 10.1111/nph.13441

[…] hus cruentus and Mirabilis jalapa, were obtained from Hatlestad et al. (). The B. vulgaris DODA and CYP76AD1 amino acid sequences were used to search against each of the 101 amino acid datasets using SWIPE v2.0.9 (Rognes, ) with an E-value cutoff of 10. We used a high E-value cutoff to maximize the sensitivity of searches in order to identify short and incomplete sequences. Positive hits with at l […]

library_books

Cache Oblivious parallel SIMD Viterbi decoding for sequence search in HMMER

2014
BMC Bioinformatics
PMCID: 4229909
PMID: 24884826
DOI: 10.1186/1471-2105-15-165

[…] vertical dependencies among cells are unlikely (although still possible), the resulting algorithm proves to be very effective in the average case.Meanwhile, Rognes proposed a different method in his Swipe tool [], which achieved even better performances than Farrar’s. Contrasting to Farrar’s, which was based on the exploitation of intra-task parallelism, Rognes’ method also makes use of SSE2 vect […]

Citations

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SWIPE institution(s)
Department of Informatics, University of Oslo, Oslo, Norway

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