PMID- 36967390
OWN - NLM
STAT- MEDLINE
DCOM- 20230328
LR  - 20230403
IS  - 1471-2105 (Electronic)
IS  - 1471-2105 (Linking)
VI  - 24
IP  - 1
DP  - 2023 Mar 26
TI  - ElasticBLAST: accelerating sequence search via cloud computing.
PG  - 117
LID - 10.1186/s12859-023-05245-9 [doi]
LID - 117
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.
CI  - (c) 2023. This is a U.S. Government work and not under copyright protection in the 
      US; foreign copyright protection may apply.
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 - Vera Alvarez, Roberto
AU  - Vera Alvarez R
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. 
      madden@ncbi.nlm.nih.gov.
LA  - eng
PT  - Journal Article
DEP - 20230326
PL  - England
TA  - BMC Bioinformatics
JT  - BMC bioinformatics
JID - 100965194
SB  - IM
UOF - bioRxiv. 2023 Jan 04;:. PMID: 36789435
MH  - *Cloud Computing
MH  - *Software
MH  - Computational Biology/methods
MH  - Databases, Factual
MH  - Costs and Cost Analysis
PMC - PMC10040096
OTO - NOTNLM
OT  - AWS Batch
OT  - Alignment
OT  - BLAST
OT  - Cloud computing
OT  - Kubernetes
COIS- The authors declare they have no competing interests.
EDAT- 2023/03/27 06:00
MHDA- 2023/03/28 19:05
PMCR- 2023/03/26
CRDT- 2023/03/26 23:14
PHST- 2023/01/04 00:00 [received]
PHST- 2023/03/21 00:00 [accepted]
PHST- 2023/03/28 19:05 [medline]
PHST- 2023/03/26 23:14 [entrez]
PHST- 2023/03/27 06:00 [pubmed]
PHST- 2023/03/26 00:00 [pmc-release]
AID - 10.1186/s12859-023-05245-9 [pii]
AID - 5245 [pii]
AID - 10.1186/s12859-023-05245-9 [doi]
PST - epublish
SO  - BMC Bioinformatics. 2023 Mar 26;24(1):117. doi: 10.1186/s12859-023-05245-9.