{"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/quickprobs-2-towards-rapid-construction-of","title":"QuickProbs 2: towards rapid construction of high-quality alignments of large protein families","arxiv_id":"1512.07437","date":"2016-08-30","proceeding":null,"authors":[],"abstract":"Increasing size of sequence databases caused by the development of high\nthroughput sequencing, poses multiple alignment algorithms to face one of the\ngreatest challenges yet. As we show, well-established techniques employed for\nincreasing alignment quality, i.e., refinement and consistency, are ineffective\nwhen large protein families are of interest. We present QuickProbs 2, an\nalgorithm for multiple sequence alignment. Based on probabilistic models,\nequipped with novel column-oriented refinement and selective consistency, it\noffers outstanding accuracy. When analysing hundreds of sequences, QuickProbs 2\nis significantly better than Clustal Omega, the previous leader for processing\nnumerous protein families. In the case of smaller sets, for which\nconsistency-based methods are the best performing, QuickProbs 2 is also\nsuperior to the competitors. Due to computational scalability of selective\nconsistency and utilisation of massively parallel architectures, presented\nalgorithm is comparable to Clustal Omega in terms of execution time, and orders\nof magnitude faster than full consistency approaches, like MSAProbs or PicXAA.\nAll these make QuickProbs 2 a useful tool for aligning families ranging from\nfew, to hundreds of proteins. QuickProbs 2 is available at\nhttps://github.com/refresh-bio/QuickProbs.","url_abs":"http://arxiv.org/abs/1512.07437v2","url_pdf":"http://arxiv.org/pdf/1512.07437v2.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":"quickprobs-2-towards-rapid-construction-of","repo_url":"https://github.com/refresh-bio/QuickProbs","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":0,"framework":"none","reach":null}],"tasks":[{"task_slug":"multiple-sequence-alignment","task_name":"Multiple Sequence Alignment"}],"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}