A Novel Partial Sequence Alignment Tool for Finding Large Deletions
Finding large deletions in genome sequences has become increasingly more useful in bioinformatics, such as in clinical research and diagnosis. Although there are a number of publically available next generation sequencing mapping and sequence alignment programs, these software packages do not correc...
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| Format: | Article |
| Language: | English |
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Wiley
2012-01-01
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| Series: | The Scientific World Journal |
| Online Access: | http://dx.doi.org/10.1100/2012/694813 |
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| author | Taner Aruk Duran Ustek Olcay Kursun |
| author_facet | Taner Aruk Duran Ustek Olcay Kursun |
| author_sort | Taner Aruk |
| collection | DOAJ |
| description | Finding large deletions in genome sequences has become increasingly more useful in bioinformatics, such as in clinical research and diagnosis. Although there are a number of publically available next generation sequencing mapping and sequence alignment programs, these software packages do not correctly align fragments containing deletions larger than one kb. We present a fast alignment software package, BinaryPartialAlign, that can be used by wet lab scientists to find long structural variations in their experiments. For BinaryPartialAlign, we make use of the Smith-Waterman (SW) algorithm with a binary-search-based approach for alignment with large gaps that we called partial alignment. BinaryPartialAlign implementation is compared with other straight-forward applications of SW. Simulation results on mtDNA fragments demonstrate the effectiveness (runtime and accuracy) of the proposed method. |
| format | Article |
| id | doaj-art-f92c182104ee454bb882c47471c90d63 |
| institution | Kabale University |
| issn | 1537-744X |
| language | English |
| publishDate | 2012-01-01 |
| publisher | Wiley |
| record_format | Article |
| series | The Scientific World Journal |
| spelling | doaj-art-f92c182104ee454bb882c47471c90d632025-02-03T01:21:29ZengWileyThe Scientific World Journal1537-744X2012-01-01201210.1100/2012/694813694813A Novel Partial Sequence Alignment Tool for Finding Large DeletionsTaner Aruk0Duran Ustek1Olcay Kursun2Scientific and Technological Research Council of Turkey (TUBITAK), 41470 Kocaeli, TurkeyGenetics Department, Institute for Experimental Medicine, Istanbul University, 34093 Istanbul, TurkeyComputer Engineering Department, Istanbul University, 34320 Istanbul, TurkeyFinding large deletions in genome sequences has become increasingly more useful in bioinformatics, such as in clinical research and diagnosis. Although there are a number of publically available next generation sequencing mapping and sequence alignment programs, these software packages do not correctly align fragments containing deletions larger than one kb. We present a fast alignment software package, BinaryPartialAlign, that can be used by wet lab scientists to find long structural variations in their experiments. For BinaryPartialAlign, we make use of the Smith-Waterman (SW) algorithm with a binary-search-based approach for alignment with large gaps that we called partial alignment. BinaryPartialAlign implementation is compared with other straight-forward applications of SW. Simulation results on mtDNA fragments demonstrate the effectiveness (runtime and accuracy) of the proposed method.http://dx.doi.org/10.1100/2012/694813 |
| spellingShingle | Taner Aruk Duran Ustek Olcay Kursun A Novel Partial Sequence Alignment Tool for Finding Large Deletions The Scientific World Journal |
| title | A Novel Partial Sequence Alignment Tool for Finding Large Deletions |
| title_full | A Novel Partial Sequence Alignment Tool for Finding Large Deletions |
| title_fullStr | A Novel Partial Sequence Alignment Tool for Finding Large Deletions |
| title_full_unstemmed | A Novel Partial Sequence Alignment Tool for Finding Large Deletions |
| title_short | A Novel Partial Sequence Alignment Tool for Finding Large Deletions |
| title_sort | novel partial sequence alignment tool for finding large deletions |
| url | http://dx.doi.org/10.1100/2012/694813 |
| work_keys_str_mv | AT taneraruk anovelpartialsequencealignmenttoolforfindinglargedeletions AT duranustek anovelpartialsequencealignmenttoolforfindinglargedeletions AT olcaykursun anovelpartialsequencealignmenttoolforfindinglargedeletions AT taneraruk novelpartialsequencealignmenttoolforfindinglargedeletions AT duranustek novelpartialsequencealignmenttoolforfindinglargedeletions AT olcaykursun novelpartialsequencealignmenttoolforfindinglargedeletions |