List of sequence alignment software: Difference between revisions

Revision as of 13:28, 26 October 2021

Revision as of 21:45, 7 December 2021

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| [[HPC-BLAST]]

| NCBI compliant multinode and multicore BLAST wrapper. Distributed with the latest version of BLAST, this wrapper facilitates parallelization of the algorithm on modern hybrid architectures with many nodes and many cores within each node. <ref>HPC-BLAST code repository https://github.com/UTennessee-JICS/HPC-BLAST</ref>|| Protein || [[Chad Burdyshaw|Burdyshaw CE]], [[Shane Sawyer|Sawyer S]], [[Mitch Horton| Horton MD]], [[Glenn Brook| Brook RG]], [[Bhanu Rekapalli| Rekapalli B]] || 2017

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| [[CS-BLAST]]

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<small><nowiki>*</nowiki>'''Sequence type:''' protein or nucleotide</small>

==Pairwise alignment==

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| SWIFOLD

| Smith-Waterman Acceleration on Intel's FPGA with OpenCL for Long DNA Sequences

|| Nucleotide || Local || E. Rucci<ref>{{Cite journal|author=Rucci, Enzo |author2=Garcia, Carlos|author3=Botella, Guillermo|author4=Naiouf, Marcelo|author5=De Giusti,Armando|author6=Prieto-Matias, Manuel|title=SWIFOLD: Smith-Waterman implementation on FPGA with OpenCL for long DNA sequences |journal=BMC Systems Biology|volume=12 | doi=10.1186/s12918-018-0614-6|doi-access=free |year=2018|issue=Suppl 5|page=96|pmid=30458766|pmc=6245597}}</ref><ref>{{Cite conference|author=Rucci, Enzo |author2=Garcia, Carlos|author3=Botella, Guillermo|author4=Naiouf, Marcelo|author5=De Giusti,Armando|author6=Prieto-Matias, Manuel|title=Accelerating Smith-Waterman Alignment of Long DNA Sequences with OpenCL on FPGA |conference=5th International Work-Conference on Bioinformatics and Biomedical Engineering |pagepages=500-511500–511 |doi=10.1007/978-3-319-56154-7_45}}</ref> || 2017-2018

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| SWIFT suit

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| ZOOM

| 100% sensitivity for a reads between 15- and 240 bp with practical mismatches. Very fast. Support insertions and deletions. Works with Illumina & SOLiD instruments, not 454.

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