SimpLiSMS: A simple, lightweight and fast approach for structured motifs searching

Ali Alatabbi; Shuhana Azmin; Md Kawser Habib; Costas S. Iliopoulos; M. Sohel Rahman

doi:10.1007/978-3-319-16480-9_22

SimpLiSMS: A simple, lightweight and fast approach for structured motifs searching

Ali Alatabbi, Shuhana Azmin, Md Kawser Habib, Costas S. Iliopoulos, M. Sohel Rahman

Informatics

Research output: Chapter in Book/Report/Conference proceeding › Conference paper › peer-review

Abstract

A Structured Motif refers to a sequence of simple motifs with distance constraints. We present SimpLiSMS, a simple, lightweight and fast algorithm for searching structured motifs. SimpLiSMS does not use any sophisticated data structure, which makes it simple and lightweight. Our experiments show excellent performance of SimpLiSMS. Furthermore, we introduce a parallel version of SimpLiSMS which runs even faster.

Original language	English
Title of host publication	Bioinformatics and Biomedical Engineering
Subtitle of host publication	Third International Conference, IWBBIO 2015, Granada, Spain, April 15-17, 2015. Proceedings, Part II
Editors	Francisco Ortuño , Ignacio Rojas
Publisher	Springer-Verlag Berlin Heidelberg
Pages	219-230
Number of pages	12
Volume	9044
ISBN (Electronic)	978-3-319-16480-9
ISBN (Print)	9783319164793
DOIs	https://doi.org/10.1007/978-3-319-16480-9_22
Publication status	Published - 2015
Event	3rd International Work-Conference on Bioinformatics and Biomedical Engineering, IWBBIO 2015 - Granada, Spain Duration: 15 Apr 2015 → 17 Apr 2015

Publication series

Name	Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume	9044
ISSN (Print)	03029743
ISSN (Electronic)	16113349

Conference

Conference	3rd International Work-Conference on Bioinformatics and Biomedical Engineering, IWBBIO 2015
Country/Territory	Spain
City	Granada
Period	15/04/2015 → 17/04/2015

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10.1007/978-3-319-16480-9_22

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Alatabbi, A., Azmin, S., Habib, M. K., Iliopoulos, C. S., & Sohel Rahman, M. (2015). SimpLiSMS: A simple, lightweight and fast approach for structured motifs searching. In F. Ortuño , & I. Rojas (Eds.), Bioinformatics and Biomedical Engineering: Third International Conference, IWBBIO 2015, Granada, Spain, April 15-17, 2015. Proceedings, Part II (Vol. 9044, pp. 219-230). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 9044). Springer-Verlag Berlin Heidelberg. https://doi.org/10.1007/978-3-319-16480-9_22

Alatabbi, Ali ; Azmin, Shuhana ; Habib, Md Kawser et al. / SimpLiSMS: A simple, lightweight and fast approach for structured motifs searching. Bioinformatics and Biomedical Engineering: Third International Conference, IWBBIO 2015, Granada, Spain, April 15-17, 2015. Proceedings, Part II. editor / Francisco Ortuño ; Ignacio Rojas. Vol. 9044 Springer-Verlag Berlin Heidelberg, 2015. pp. 219-230 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)).

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abstract = "A Structured Motif refers to a sequence of simple motifs with distance constraints. We present SimpLiSMS, a simple, lightweight and fast algorithm for searching structured motifs. SimpLiSMS does not use any sophisticated data structure, which makes it simple and lightweight. Our experiments show excellent performance of SimpLiSMS. Furthermore, we introduce a parallel version of SimpLiSMS which runs even faster.",

author = "Ali Alatabbi and Shuhana Azmin and Habib, {Md Kawser} and Iliopoulos, {Costas S.} and {Sohel Rahman}, M.",

year = "2015",

doi = "10.1007/978-3-319-16480-9_22",

language = "English",

isbn = "9783319164793",

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series = "Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)",

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pages = "219--230",

editor = "{Ortu{\~n}o }, Francisco and Ignacio Rojas",

booktitle = "Bioinformatics and Biomedical Engineering",

note = "3rd International Work-Conference on Bioinformatics and Biomedical Engineering, IWBBIO 2015 ; Conference date: 15-04-2015 Through 17-04-2015",

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Alatabbi, A, Azmin, S, Habib, MK, Iliopoulos, CS & Sohel Rahman, M 2015, SimpLiSMS: A simple, lightweight and fast approach for structured motifs searching. in F Ortuño & I Rojas (eds), Bioinformatics and Biomedical Engineering: Third International Conference, IWBBIO 2015, Granada, Spain, April 15-17, 2015. Proceedings, Part II. vol. 9044, Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 9044, Springer-Verlag Berlin Heidelberg, pp. 219-230, 3rd International Work-Conference on Bioinformatics and Biomedical Engineering, IWBBIO 2015, Granada, Spain, 15/04/2015. https://doi.org/10.1007/978-3-319-16480-9_22

SimpLiSMS: A simple, lightweight and fast approach for structured motifs searching. / Alatabbi, Ali; Azmin, Shuhana; Habib, Md Kawser et al.
Bioinformatics and Biomedical Engineering: Third International Conference, IWBBIO 2015, Granada, Spain, April 15-17, 2015. Proceedings, Part II. ed. / Francisco Ortuño ; Ignacio Rojas. Vol. 9044 Springer-Verlag Berlin Heidelberg, 2015. p. 219-230 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 9044).

Research output: Chapter in Book/Report/Conference proceeding › Conference paper › peer-review

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AU - Iliopoulos, Costas S.

AU - Sohel Rahman, M.

PY - 2015

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AB - A Structured Motif refers to a sequence of simple motifs with distance constraints. We present SimpLiSMS, a simple, lightweight and fast algorithm for searching structured motifs. SimpLiSMS does not use any sophisticated data structure, which makes it simple and lightweight. Our experiments show excellent performance of SimpLiSMS. Furthermore, we introduce a parallel version of SimpLiSMS which runs even faster.

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DO - 10.1007/978-3-319-16480-9_22

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Alatabbi A, Azmin S, Habib MK, Iliopoulos CS, Sohel Rahman M. SimpLiSMS: A simple, lightweight and fast approach for structured motifs searching. In Ortuño F, Rojas I, editors, Bioinformatics and Biomedical Engineering: Third International Conference, IWBBIO 2015, Granada, Spain, April 15-17, 2015. Proceedings, Part II. Vol. 9044. Springer-Verlag Berlin Heidelberg. 2015. p. 219-230. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)). doi: 10.1007/978-3-319-16480-9_22

SimpLiSMS: A simple, lightweight and fast approach for structured motifs searching

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