Tuyển tập các báo cáo nghiên cứu về sinh học được đăng trên tạp chí y học Molecular Biology cung cấp cho các bạn kiến thức về ngành sinh học đề tài: A basic analysis toolkit for biological sequences. | Algorithms for Molecular Biology BioMed Central Software article Open Access A basic analysis toolkit for biological sequences Raffaele Giancarlo Alessandro Siragusa Enrico Siragusa and Filippo Utro Address Dipartimento di Matematica Applicazioni Università di Palermo Italy Email Raffaele Giancarlo - raffaele@ Alessandro Siragusa - Enrico Siragusa - enricos@ Filippo Utro - Corresponding author Published 18 September 2007 Received 7 May 2007 Algorithms for Molecular Biology 2007 2 10 doi 1748-7188-2-10 Accepted 18 September 2007 This article is available from http content 2 1 10 2007 Giancarlo et al licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License http licenses by which permits unrestricted use distribution and reproduction in any medium provided the original work is properly cited. Abstract This paper presents a software library nicknamed BATS for some basic sequence analysis tasks. Namely local alignments via approximate string matching and global alignments via longest common subsequence and alignments with affine and concave gap cost functions. Moreover it also supports filtering operations to select strings from a set and establish their statistical significance via z-score computation. None of the algorithms is new but although they are generally regarded as fundamental for sequence analysis they have not been implemented in a single and consistent software package as we do here. Therefore our main contribution is to fill this gap between algorithmic theory and practice by providing an extensible and easy to use software library that includes algorithms for the mentioned string matching and alignment problems. The library consists of C C library functions as well as Perl library functions. It can be interfaced with Bioperl and can also be used as a stand-alone .
