These tools will no longer be maintained as of December 31, 2024. Archived website can be found here. PubMed4Hh GitHub repository can be found here. Contact NLM Customer Service if you have questions.
2. CUDASW++ 3.0: accelerating Smith-Waterman protein database search by coupling CPU and GPU SIMD instructions. Liu Y; Wirawan A; Schmidt B BMC Bioinformatics; 2013 Apr; 14():117. PubMed ID: 23557111 [TBL] [Abstract][Full Text] [Related]
3. Pairwise statistical significance of local sequence alignment using sequence-specific and position-specific substitution matrices. Agrawal A; Huang X IEEE/ACM Trans Comput Biol Bioinform; 2011; 8(1):194-205. PubMed ID: 21071807 [TBL] [Abstract][Full Text] [Related]
4. Parallel Implementation of MAFFT on CUDA-Enabled Graphics Hardware. Zhu X; Li K; Salah A; Shi L; Li K IEEE/ACM Trans Comput Biol Bioinform; 2015; 12(1):205-18. PubMed ID: 26357090 [TBL] [Abstract][Full Text] [Related]
5. Protein alignment algorithms with an efficient backtracking routine on multiple GPUs. Blazewicz J; Frohmberg W; Kierzynka M; Pesch E; Wojciechowski P BMC Bioinformatics; 2011 May; 12():181. PubMed ID: 21599912 [TBL] [Abstract][Full Text] [Related]
6. GPU accelerated sequence alignment with traceback for GATK HaplotypeCaller. Ren S; Ahmed N; Bertels K; Al-Ars Z BMC Genomics; 2019 Apr; 20(Suppl 2):184. PubMed ID: 30967111 [TBL] [Abstract][Full Text] [Related]
7. Pairwise sequence alignment for very long sequences on GPUs. Li J; Ranka S; Sahni S Int J Bioinform Res Appl; 2014; 10(4-5):345-68. PubMed ID: 24989857 [TBL] [Abstract][Full Text] [Related]
8. cuBLASTP: Fine-Grained Parallelization of Protein Sequence Search on CPU+GPU. Zhang J; Wang H; Feng WC IEEE/ACM Trans Comput Biol Bioinform; 2017; 14(4):830-843. PubMed ID: 26469393 [TBL] [Abstract][Full Text] [Related]
16. GASAL2: a GPU accelerated sequence alignment library for high-throughput NGS data. Ahmed N; Lévy J; Ren S; Mushtaq H; Bertels K; Al-Ars Z BMC Bioinformatics; 2019 Oct; 20(1):520. PubMed ID: 31653208 [TBL] [Abstract][Full Text] [Related]
17. CUDA-BLASTP: accelerating BLASTP on CUDA-enabled graphics hardware. Liu W; Schmidt B; Müller-Wittig W IEEE/ACM Trans Comput Biol Bioinform; 2011; 8(6):1678-84. PubMed ID: 21339531 [TBL] [Abstract][Full Text] [Related]
18. Coupling SIMD and SIMT architectures to boost performance of a phylogeny-aware alignment kernel. Alachiotis N; Berger SA; Stamatakis A BMC Bioinformatics; 2012 Aug; 13():196. PubMed ID: 22876807 [TBL] [Abstract][Full Text] [Related]
19. Pairwise statistical significance and empirical determination of effective gap opening penalties for protein local sequence alignment. Agrawal A; Brendel VP; Huang X Int J Comput Biol Drug Des; 2008; 1(4):347-67. PubMed ID: 20063463 [TBL] [Abstract][Full Text] [Related]