UNION: An Efficient Mapping Tool Using UniMark with Non-overlapping Interval Indexing Strategy View Full Text


Ontology type: schema:Chapter     


Chapter Info

DATE

2011

AUTHORS

Che-Lun Hung , Chun-Yuan Lin , Yu-Chen Hu

ABSTRACT

NGS has become a popular research field in biologists because it was able to produce inexpensive and accuracy short biology sequences very fast. NGS technique has been improved to produce long length sequences, more than 100bp, recently with the same quality, accuracy and speed. Thus, tools for short sequences may be not suitable for long length sequences. We propose a new tool called UNION for re-sequencing applications by mapping long length sequences to a reference genome. UNION uses the UniMarker with a non-overlapping interval indexing strategy and a tool, CORAL, to do sequence alignments. For the experiments we randomly cut ten thousands sequences with a length of 512bp from the genome of Trichomonas and also produce mutations/sequence errors for these sequences to simulate different similarities. UNION has been compared with GMAP in terms of speed and accuracy and achieves better performance than that of GMAP. More... »

PAGES

187-196

Book

TITLE

Database Theory and Application, Bio-Science and Bio-Technology

ISBN

978-3-642-27156-4
978-3-642-27157-1

Identifiers

URI

http://scigraph.springernature.com/pub.10.1007/978-3-642-27157-1_21

DOI

http://dx.doi.org/10.1007/978-3-642-27157-1_21

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1000216520


Indexing Status Check whether this publication has been indexed by Scopus and Web Of Science using the SN Indexing Status Tool
Incoming Citations Browse incoming citations for this publication using opencitations.net

JSON-LD is the canonical representation for SciGraph data.

TIP: You can open this SciGraph record using an external JSON-LD service: JSON-LD Playground Google SDTT

[
  {
    "@context": "https://springernature.github.io/scigraph/jsonld/sgcontext.json", 
    "about": [
      {
        "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/0604", 
        "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
        "name": "Genetics", 
        "type": "DefinedTerm"
      }, 
      {
        "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/06", 
        "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
        "name": "Biological Sciences", 
        "type": "DefinedTerm"
      }
    ], 
    "author": [
      {
        "affiliation": {
          "alternateName": "Providence University", 
          "id": "https://www.grid.ac/institutes/grid.412550.7", 
          "name": [
            "Dept. of Computer Science & Communication Engineering, Providence University, 200 Chung Chi Rd., Taichung, 43301, Republic of China, Taiwan"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Hung", 
        "givenName": "Che-Lun", 
        "id": "sg:person.01336120166.62", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01336120166.62"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Chang Gung University", 
          "id": "https://www.grid.ac/institutes/grid.145695.a", 
          "name": [
            "Dept. of Computer Science & Information Engineering, Chang Gung University, 259 Wen-Hwa 1st Road, Kwei-Shan Tao-Yuan, 333, Republic of China, Taiwan"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Lin", 
        "givenName": "Chun-Yuan", 
        "id": "sg:person.0665540554.26", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0665540554.26"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Providence University", 
          "id": "https://www.grid.ac/institutes/grid.412550.7", 
          "name": [
            "Dept. of Computer Science & Information Management, Providence University, 200 Chung Chi Rd., Taichung, 43301, Republic of China, Taiwan"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Hu", 
        "givenName": "Yu-Chen", 
        "id": "sg:person.012113441135.19", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.012113441135.19"
        ], 
        "type": "Person"
      }
    ], 
    "citation": [
      {
        "id": "https://doi.org/10.1016/s0022-2836(05)80360-2", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1013618994"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/bioinformatics/bti310", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1015580011"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/bioinformatics/13.1.75", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1016756233"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1101/gr.224502", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1023120786"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/nar/27.11.2369", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1041672956"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1089/10665270050081478", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1059204834"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1101/gr.7.6.649", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1083108595"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1101/gr.8.9.967", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1083321060"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1109/csb.2003.1227409", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1095088143"
        ], 
        "type": "CreativeWork"
      }
    ], 
    "datePublished": "2011", 
    "datePublishedReg": "2011-01-01", 
    "description": "NGS has become a popular research field in biologists because it was able to produce inexpensive and accuracy short biology sequences very fast. NGS technique has been improved to produce long length sequences, more than 100bp, recently with the same quality, accuracy and speed. Thus, tools for short sequences may be not suitable for long length sequences. We propose a new tool called UNION for re-sequencing applications by mapping long length sequences to a reference genome. UNION uses the UniMarker with a non-overlapping interval indexing strategy and a tool, CORAL, to do sequence alignments. For the experiments we randomly cut ten thousands sequences with a length of 512bp from the genome of Trichomonas and also produce mutations/sequence errors for these sequences to simulate different similarities. UNION has been compared with GMAP in terms of speed and accuracy and achieves better performance than that of GMAP.", 
    "editor": [
      {
        "familyName": "Kim", 
        "givenName": "Tai-hoon", 
        "type": "Person"
      }, 
      {
        "familyName": "Adeli", 
        "givenName": "Hojjat", 
        "type": "Person"
      }, 
      {
        "familyName": "Cuzzocrea", 
        "givenName": "Alfredo", 
        "type": "Person"
      }, 
      {
        "familyName": "Arslan", 
        "givenName": "Tughrul", 
        "type": "Person"
      }, 
      {
        "familyName": "Zhang", 
        "givenName": "Yanchun", 
        "type": "Person"
      }, 
      {
        "familyName": "Ma", 
        "givenName": "Jianhua", 
        "type": "Person"
      }, 
      {
        "familyName": "Chung", 
        "givenName": "Kyo-il", 
        "type": "Person"
      }, 
      {
        "familyName": "Mariyam", 
        "givenName": "Siti", 
        "type": "Person"
      }, 
      {
        "familyName": "Song", 
        "givenName": "Xiaofeng", 
        "type": "Person"
      }
    ], 
    "genre": "chapter", 
    "id": "sg:pub.10.1007/978-3-642-27157-1_21", 
    "inLanguage": [
      "en"
    ], 
    "isAccessibleForFree": false, 
    "isPartOf": {
      "isbn": [
        "978-3-642-27156-4", 
        "978-3-642-27157-1"
      ], 
      "name": "Database Theory and Application, Bio-Science and Bio-Technology", 
      "type": "Book"
    }, 
    "name": "UNION: An Efficient Mapping Tool Using UniMark with Non-overlapping Interval Indexing Strategy", 
    "pagination": "187-196", 
    "productId": [
      {
        "name": "doi", 
        "type": "PropertyValue", 
        "value": [
          "10.1007/978-3-642-27157-1_21"
        ]
      }, 
      {
        "name": "readcube_id", 
        "type": "PropertyValue", 
        "value": [
          "01076528f14a27d1bb3f97781295d41244d8752827d508bd2a7ce82a833a97e2"
        ]
      }, 
      {
        "name": "dimensions_id", 
        "type": "PropertyValue", 
        "value": [
          "pub.1000216520"
        ]
      }
    ], 
    "publisher": {
      "location": "Berlin, Heidelberg", 
      "name": "Springer Berlin Heidelberg", 
      "type": "Organisation"
    }, 
    "sameAs": [
      "https://doi.org/10.1007/978-3-642-27157-1_21", 
      "https://app.dimensions.ai/details/publication/pub.1000216520"
    ], 
    "sdDataset": "chapters", 
    "sdDatePublished": "2019-04-15T18:15", 
    "sdLicense": "https://scigraph.springernature.com/explorer/license/", 
    "sdPublisher": {
      "name": "Springer Nature - SN SciGraph project", 
      "type": "Organization"
    }, 
    "sdSource": "s3://com-uberresearch-data-dimensions-target-20181106-alternative/cleanup/v134/2549eaecd7973599484d7c17b260dba0a4ecb94b/merge/v9/a6c9fde33151104705d4d7ff012ea9563521a3ce/jats-lookup/v90/0000000001_0000000264/records_8681_00000282.jsonl", 
    "type": "Chapter", 
    "url": "http://link.springer.com/10.1007/978-3-642-27157-1_21"
  }
]
 

Download the RDF metadata as:  json-ld nt turtle xml License info

HOW TO GET THIS DATA PROGRAMMATICALLY:

JSON-LD is a popular format for linked data which is fully compatible with JSON.

curl -H 'Accept: application/ld+json' 'https://scigraph.springernature.com/pub.10.1007/978-3-642-27157-1_21'

N-Triples is a line-based linked data format ideal for batch operations.

curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1007/978-3-642-27157-1_21'

Turtle is a human-readable linked data format.

curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1007/978-3-642-27157-1_21'

RDF/XML is a standard XML format for linked data.

curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1007/978-3-642-27157-1_21'


 

This table displays all metadata directly associated to this object as RDF triples.

150 TRIPLES      23 PREDICATES      36 URIs      20 LITERALS      8 BLANK NODES

Subject Predicate Object
1 sg:pub.10.1007/978-3-642-27157-1_21 schema:about anzsrc-for:06
2 anzsrc-for:0604
3 schema:author N366fe37b2eeb4d7ab9942e8eb1b9ca8c
4 schema:citation https://doi.org/10.1016/s0022-2836(05)80360-2
5 https://doi.org/10.1089/10665270050081478
6 https://doi.org/10.1093/bioinformatics/13.1.75
7 https://doi.org/10.1093/bioinformatics/bti310
8 https://doi.org/10.1093/nar/27.11.2369
9 https://doi.org/10.1101/gr.224502
10 https://doi.org/10.1101/gr.7.6.649
11 https://doi.org/10.1101/gr.8.9.967
12 https://doi.org/10.1109/csb.2003.1227409
13 schema:datePublished 2011
14 schema:datePublishedReg 2011-01-01
15 schema:description NGS has become a popular research field in biologists because it was able to produce inexpensive and accuracy short biology sequences very fast. NGS technique has been improved to produce long length sequences, more than 100bp, recently with the same quality, accuracy and speed. Thus, tools for short sequences may be not suitable for long length sequences. We propose a new tool called UNION for re-sequencing applications by mapping long length sequences to a reference genome. UNION uses the UniMarker with a non-overlapping interval indexing strategy and a tool, CORAL, to do sequence alignments. For the experiments we randomly cut ten thousands sequences with a length of 512bp from the genome of Trichomonas and also produce mutations/sequence errors for these sequences to simulate different similarities. UNION has been compared with GMAP in terms of speed and accuracy and achieves better performance than that of GMAP.
16 schema:editor Nc3d3388a64e44118942565a325a2571a
17 schema:genre chapter
18 schema:inLanguage en
19 schema:isAccessibleForFree false
20 schema:isPartOf Ncbcd5f97d12d4dbaa2f0d67a1339248a
21 schema:name UNION: An Efficient Mapping Tool Using UniMark with Non-overlapping Interval Indexing Strategy
22 schema:pagination 187-196
23 schema:productId N79b90f176ba449b5aa418d1ea761ba78
24 N95748dc3446b49ec8024b656cf6e124d
25 Nda26472c188e4129913d494476570c20
26 schema:publisher N67f0952efc6f475ba86f67e05742a4a6
27 schema:sameAs https://app.dimensions.ai/details/publication/pub.1000216520
28 https://doi.org/10.1007/978-3-642-27157-1_21
29 schema:sdDatePublished 2019-04-15T18:15
30 schema:sdLicense https://scigraph.springernature.com/explorer/license/
31 schema:sdPublisher N326a5047713a45ceb50b31dc7fea7442
32 schema:url http://link.springer.com/10.1007/978-3-642-27157-1_21
33 sgo:license sg:explorer/license/
34 sgo:sdDataset chapters
35 rdf:type schema:Chapter
36 N06795f013d0f4b219c5a6acd1f533cfc schema:familyName Mariyam
37 schema:givenName Siti
38 rdf:type schema:Person
39 N07beaa8bf6bf4ab69e41f63d67da6f8e schema:familyName Cuzzocrea
40 schema:givenName Alfredo
41 rdf:type schema:Person
42 N11973f96eab140a4b7fb07c88d3f1ab9 schema:familyName Song
43 schema:givenName Xiaofeng
44 rdf:type schema:Person
45 N17161877156f4d8092512315b43e1d55 schema:familyName Kim
46 schema:givenName Tai-hoon
47 rdf:type schema:Person
48 N1e77e422ff054d62aec98277dd55fdd1 schema:familyName Chung
49 schema:givenName Kyo-il
50 rdf:type schema:Person
51 N2850513ab43e40ee9f7b99ea2fd64d50 rdf:first N11973f96eab140a4b7fb07c88d3f1ab9
52 rdf:rest rdf:nil
53 N2b0be6c625704687b6f18296169edfd1 rdf:first N06795f013d0f4b219c5a6acd1f533cfc
54 rdf:rest N2850513ab43e40ee9f7b99ea2fd64d50
55 N326a5047713a45ceb50b31dc7fea7442 schema:name Springer Nature - SN SciGraph project
56 rdf:type schema:Organization
57 N366fe37b2eeb4d7ab9942e8eb1b9ca8c rdf:first sg:person.01336120166.62
58 rdf:rest Ncad42fb3109841cf88a699e2ac1f3ca3
59 N4c1c48f262be4dc7874f49cea580b431 schema:familyName Adeli
60 schema:givenName Hojjat
61 rdf:type schema:Person
62 N4d6fd636a02a426facb0c9b57085cd58 rdf:first N6407bda8740c417d8c8fefa10a7f30dc
63 rdf:rest N9e8a34c44eac4cceb6cd169827dd7896
64 N6407bda8740c417d8c8fefa10a7f30dc schema:familyName Arslan
65 schema:givenName Tughrul
66 rdf:type schema:Person
67 N67f0952efc6f475ba86f67e05742a4a6 schema:location Berlin, Heidelberg
68 schema:name Springer Berlin Heidelberg
69 rdf:type schema:Organisation
70 N6f9c673fbf5948e89bffdffb52d8ae7a rdf:first N07beaa8bf6bf4ab69e41f63d67da6f8e
71 rdf:rest N4d6fd636a02a426facb0c9b57085cd58
72 N727573e017f946eb9ef21d8dcf85f2ee rdf:first sg:person.012113441135.19
73 rdf:rest rdf:nil
74 N79b90f176ba449b5aa418d1ea761ba78 schema:name doi
75 schema:value 10.1007/978-3-642-27157-1_21
76 rdf:type schema:PropertyValue
77 N7f31142df4c24717989f22b42345f38d rdf:first N4c1c48f262be4dc7874f49cea580b431
78 rdf:rest N6f9c673fbf5948e89bffdffb52d8ae7a
79 N8cc789fcc7f247c79496589257233d79 rdf:first Nc164d9911cd449b78ab82c7984663ba9
80 rdf:rest Nfefc75429a324166ad82edeba62940f4
81 N95748dc3446b49ec8024b656cf6e124d schema:name dimensions_id
82 schema:value pub.1000216520
83 rdf:type schema:PropertyValue
84 N9e8a34c44eac4cceb6cd169827dd7896 rdf:first Ne0269c73a4564f0881e5640cadca3555
85 rdf:rest N8cc789fcc7f247c79496589257233d79
86 Nc164d9911cd449b78ab82c7984663ba9 schema:familyName Ma
87 schema:givenName Jianhua
88 rdf:type schema:Person
89 Nc3d3388a64e44118942565a325a2571a rdf:first N17161877156f4d8092512315b43e1d55
90 rdf:rest N7f31142df4c24717989f22b42345f38d
91 Ncad42fb3109841cf88a699e2ac1f3ca3 rdf:first sg:person.0665540554.26
92 rdf:rest N727573e017f946eb9ef21d8dcf85f2ee
93 Ncbcd5f97d12d4dbaa2f0d67a1339248a schema:isbn 978-3-642-27156-4
94 978-3-642-27157-1
95 schema:name Database Theory and Application, Bio-Science and Bio-Technology
96 rdf:type schema:Book
97 Nda26472c188e4129913d494476570c20 schema:name readcube_id
98 schema:value 01076528f14a27d1bb3f97781295d41244d8752827d508bd2a7ce82a833a97e2
99 rdf:type schema:PropertyValue
100 Ne0269c73a4564f0881e5640cadca3555 schema:familyName Zhang
101 schema:givenName Yanchun
102 rdf:type schema:Person
103 Nfefc75429a324166ad82edeba62940f4 rdf:first N1e77e422ff054d62aec98277dd55fdd1
104 rdf:rest N2b0be6c625704687b6f18296169edfd1
105 anzsrc-for:06 schema:inDefinedTermSet anzsrc-for:
106 schema:name Biological Sciences
107 rdf:type schema:DefinedTerm
108 anzsrc-for:0604 schema:inDefinedTermSet anzsrc-for:
109 schema:name Genetics
110 rdf:type schema:DefinedTerm
111 sg:person.012113441135.19 schema:affiliation https://www.grid.ac/institutes/grid.412550.7
112 schema:familyName Hu
113 schema:givenName Yu-Chen
114 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.012113441135.19
115 rdf:type schema:Person
116 sg:person.01336120166.62 schema:affiliation https://www.grid.ac/institutes/grid.412550.7
117 schema:familyName Hung
118 schema:givenName Che-Lun
119 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01336120166.62
120 rdf:type schema:Person
121 sg:person.0665540554.26 schema:affiliation https://www.grid.ac/institutes/grid.145695.a
122 schema:familyName Lin
123 schema:givenName Chun-Yuan
124 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0665540554.26
125 rdf:type schema:Person
126 https://doi.org/10.1016/s0022-2836(05)80360-2 schema:sameAs https://app.dimensions.ai/details/publication/pub.1013618994
127 rdf:type schema:CreativeWork
128 https://doi.org/10.1089/10665270050081478 schema:sameAs https://app.dimensions.ai/details/publication/pub.1059204834
129 rdf:type schema:CreativeWork
130 https://doi.org/10.1093/bioinformatics/13.1.75 schema:sameAs https://app.dimensions.ai/details/publication/pub.1016756233
131 rdf:type schema:CreativeWork
132 https://doi.org/10.1093/bioinformatics/bti310 schema:sameAs https://app.dimensions.ai/details/publication/pub.1015580011
133 rdf:type schema:CreativeWork
134 https://doi.org/10.1093/nar/27.11.2369 schema:sameAs https://app.dimensions.ai/details/publication/pub.1041672956
135 rdf:type schema:CreativeWork
136 https://doi.org/10.1101/gr.224502 schema:sameAs https://app.dimensions.ai/details/publication/pub.1023120786
137 rdf:type schema:CreativeWork
138 https://doi.org/10.1101/gr.7.6.649 schema:sameAs https://app.dimensions.ai/details/publication/pub.1083108595
139 rdf:type schema:CreativeWork
140 https://doi.org/10.1101/gr.8.9.967 schema:sameAs https://app.dimensions.ai/details/publication/pub.1083321060
141 rdf:type schema:CreativeWork
142 https://doi.org/10.1109/csb.2003.1227409 schema:sameAs https://app.dimensions.ai/details/publication/pub.1095088143
143 rdf:type schema:CreativeWork
144 https://www.grid.ac/institutes/grid.145695.a schema:alternateName Chang Gung University
145 schema:name Dept. of Computer Science & Information Engineering, Chang Gung University, 259 Wen-Hwa 1st Road, Kwei-Shan Tao-Yuan, 333, Republic of China, Taiwan
146 rdf:type schema:Organization
147 https://www.grid.ac/institutes/grid.412550.7 schema:alternateName Providence University
148 schema:name Dept. of Computer Science & Communication Engineering, Providence University, 200 Chung Chi Rd., Taichung, 43301, Republic of China, Taiwan
149 Dept. of Computer Science & Information Management, Providence University, 200 Chung Chi Rd., Taichung, 43301, Republic of China, Taiwan
150 rdf:type schema:Organization
 




Preview window. Press ESC to close (or click here)


...