{"about":{"site":"https://codewithpapers.app","non_affiliation":"Code with Papers and Syntology are not affiliated with, endorsed by, or sponsored by Papers with Code, Meta, or the pwc-archive mirror.","licence":"CC BY-SA 4.0","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","attribution":"https://codewithpapers.app/attribution","modified":"archive material modified by Syntology; see the attribution page"},"url":"/paper/genoogle-an-indexed-and-parallelized-search","title":"Genoogle: an indexed and parallelized search engine for similar DNA sequences","arxiv_id":"1507.02987","date":"2015-07-10","proceeding":null,"authors":["Albrecht Felipe"],"abstract":"The search for similar genetic sequences is one of the main bioinformatics\ntasks. The genetic sequences data banks are growing exponentially and the\nsearching techniques that use linear time are not capable to do the search in\nthe required time anymore. Another problem is that the clock speed of the\nmodern processors are not growing as it did before, instead, the processing\ncapacity is growing with the addiction of more processing cores and the\ntechniques which does not use parallel computing does not have benefits from\nthese extra cores. This work aims to use data indexing techniques to reduce the\nsearching process computation cost united with the parallelization of the\nsearching techniques to use the computational capacity of the multi core\nprocessors. To verify the viability of using these two techniques\nsimultaneously, a software which uses parallelization techniques with inverted\nindexes was developed.\n  Experiments were executed to analyze the performance gain when parallelism is\nutilized, the search time gain, and also the quality of the results when it\ncompared with others searching tools. The results of these experiments were\npromising, the parallelism gain overcame the expected speedup, the searching\ntime was 20 times faster than the parallelized NCBI BLAST, and the searching\nresults showed a good quality when compared with this tool.\n  The software source code is available at\nhttps://github.com/felipealbrecht/Genoogle .","url_abs":"http://arxiv.org/abs/1507.02987v1","url_pdf":"http://arxiv.org/pdf/1507.02987v1.pdf","source":{"archive":"pwc-archive (Hugging Face), CC BY-SA 4.0","snapshot":"2025-07-28","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","row_kind":"abstracts"},"code_links":[{"paper_slug":"genoogle-an-indexed-and-parallelized-search","repo_url":"https://github.com/felipealbrecht/Genoogle","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":0,"framework":"jax","reach":null}],"tasks":[],"methods":[],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"syntology_url":null,"atlas_url":null,"mcp":null,"developers":"https://syntology.ai/developers"},"arxiv_metadata":null,"syntology_extracted_results":null}