PMID- 36789435
OWN - NLM
STAT- PubMed-not-MEDLINE
LR  - 20230403
DP  - 2023 Jan 4
TI  - ElasticBLAST: Accelerating Sequence Search via Cloud Computing.
LID - 2023.01.04.522777 [pii]
LID - 10.1101/2023.01.04.522777 [doi]
AB  - BACKGROUND: Biomedical researchers use alignments produced by BLAST (Basic Local 
      Alignment Search Tool) to categorize their query sequences. Producing such 
      alignments is an essential bioinformatics task that is well suited for the cloud. 
      The cloud can perform many calculations quickly as well as store and access large 
      volumes of data. Bioinformaticians can also use it to collaborate with other 
      researchers, sharing their results, datasets and even their pipelines on a common 
      platform. RESULTS: We present ElasticBLAST, a cloud native application to perform 
      BLAST alignments in the cloud. ElasticBLAST can handle anywhere from a few to 
      many thousands of queries and run the searches on thousands of virtual CPUs (if 
      desired), deleting resources when it is done. It uses cloud native tools for 
      orchestration and can request discounted instances, lowering cloud costs for 
      users. It is supported on Amazon Web Services and Google Cloud Platform. It can 
      search BLAST databases that are user provided or from the National Center for 
      Biotechnology Information. CONCLUSION: We show that ElasticBLAST is a useful 
      application that can efficiently perform BLAST searches for the user in the 
      cloud, demonstrating that with two examples. At the same time, it hides much of 
      the complexity of working in the cloud, lowering the threshold to move work to 
      the cloud.
FAU - Camacho, Christiam
AU  - Camacho C
AD  - National Center for Biotechnology Information, National Library of Medicine, 
      National Institutes of Health, 8600 Rockville Pike, Bethesda, MD, 20894, USA.
FAU - Boratyn, Grzegorz M
AU  - Boratyn GM
AD  - National Center for Biotechnology Information, National Library of Medicine, 
      National Institutes of Health, 8600 Rockville Pike, Bethesda, MD, 20894, USA.
FAU - Joukov, Victor
AU  - Joukov V
AD  - National Center for Biotechnology Information, National Library of Medicine, 
      National Institutes of Health, 8600 Rockville Pike, Bethesda, MD, 20894, USA.
FAU - Alvarez, Roberto Vera
AU  - Alvarez RV
AD  - National Center for Biotechnology Information, National Library of Medicine, 
      National Institutes of Health, 8600 Rockville Pike, Bethesda, MD, 20894, USA.
FAU - Madden, Thomas L
AU  - Madden TL
AD  - National Center for Biotechnology Information, National Library of Medicine, 
      National Institutes of Health, 8600 Rockville Pike, Bethesda, MD, 20894, USA.
LA  - eng
PT  - Preprint
DEP - 20230104
PL  - United States
TA  - bioRxiv
JT  - bioRxiv : the preprint server for biology
JID - 101680187
UIN - BMC Bioinformatics. 2023 Mar 26;24(1):117. PMID: 36967390
PMC - PMC9928022
COIS- Competing Interests: The authors declare they have no competing interests.
EDAT- 2023/02/16 06:00
MHDA- 2023/02/16 06:01
PMCR- 2023/02/14
CRDT- 2023/02/15 02:13
PHST- 2023/02/15 02:13 [entrez]
PHST- 2023/02/16 06:00 [pubmed]
PHST- 2023/02/16 06:01 [medline]
PHST- 2023/02/14 00:00 [pmc-release]
AID - 2023.01.04.522777 [pii]
AID - 10.1101/2023.01.04.522777 [doi]
PST - epublish
SO  - bioRxiv [Preprint]. 2023 Jan 4:2023.01.04.522777. doi: 10.1101/2023.01.04.522777.