Loading…
Pairwise end sequencing: a unified approach to genomic mapping and sequencing
Strategies for large-scale genomic DNA sequencing currently require physical mapping, followed by detailed mapping, and finally sequencing. The level of mapping detail determines the amount of effort, or sequence redundancy, required to finish a project. Current strategies attempt to find a balance...
Saved in:
Published in: | Genomics (San Diego, Calif.) Calif.), 1995-03, Vol.26 (2), p.345-353 |
---|---|
Main Authors: | , , , |
Format: | Article |
Language: | English |
Subjects: | |
Citations: | Items that this one cites Items that cite this one |
Online Access: | Get full text |
Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
cited_by | cdi_FETCH-LOGICAL-c487t-dd4ce0fe3589088ec93b26f337d59edfaf0f54a654ab6411e89a215c1bba16bb3 |
---|---|
cites | cdi_FETCH-LOGICAL-c487t-dd4ce0fe3589088ec93b26f337d59edfaf0f54a654ab6411e89a215c1bba16bb3 |
container_end_page | 353 |
container_issue | 2 |
container_start_page | 345 |
container_title | Genomics (San Diego, Calif.) |
container_volume | 26 |
creator | Roach, Jared C. Boysen, Cecilie Wang, Kai Hood, Leroy |
description | Strategies for large-scale genomic DNA sequencing currently require physical mapping, followed by detailed mapping, and finally sequencing. The level of mapping detail determines the amount of effort, or sequence redundancy, required to finish a project. Current strategies attempt to find a balance between mapping and sequencing efforts. One such approach is to employ strategies that use sequence data to build physical maps. Such maps alleviate the need for prior mapping and reduce the final required sequence redundancy. To this end, the utility of correlating pairs of sequence data derived from both ends of subcloned templates is well recognized. However, optimal strategies employing such pairwise data have not been established. In the present work, we simulate and analyze the parameters of pairwise sequencing projects including template length, sequence read length, and total sequence redundancy. One pairwise strategy based on sequencing both ends of plasmid subclones is recommended and illustrated with raw data simulations. We find that pairwise strategies are effective with both small (cosmid) and large (megaYAC) targets and produce ordered sequence data with a high level of mapping completeness. They are ideal for fine-scale mapping and gene finding and as initial steps for either a high- or a low-redundancy sequencing effort. Such strategies are highly automatable. |
doi_str_mv | 10.1016/0888-7543(95)80219-C |
format | article |
fullrecord | <record><control><sourceid>proquest_cross</sourceid><recordid>TN_cdi_proquest_miscellaneous_77376513</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><els_id>088875439580219C</els_id><sourcerecordid>77376513</sourcerecordid><originalsourceid>FETCH-LOGICAL-c487t-dd4ce0fe3589088ec93b26f337d59edfaf0f54a654ab6411e89a215c1bba16bb3</originalsourceid><addsrcrecordid>eNp9kF1rFDEUhkOx1LX6DyrmQsRejCaTj0m8EGTRVmhRaHsdziQn25SdmW2ya_Hfm3WXBW-8CIGc55zz5iHkjLMPnHH9kRljmk5J8d6qc8Nabpv5EZlxZmxjtNTPyOyAPCcvSnlgjFlh2hNy0mnGpeYzcv0TUn5KBSmOgRZ83ODo07j4RIFuxhQTBgqrVZ7A39P1RBc4TkPydKiPFaPwT9dLchxhWfDV_j4ld9--3s4vm6sfF9_nX64aL023bkKQHllEoYytEdFb0bc6CtEFZTFEiCwqCbqeXkvO0VhoufK874Hrvhen5N1ubg1Wd5e1G1LxuFzCiNOmuK4TnVZcVFDuQJ-nUjJGt8ppgPzbcea2Ft1Wkdsqcla5vxbdvLa93s_f9AOGQ9NeW62_3deheFjGDPX75YAJxZjR2-1vdliEycEiV-TupmVcMK5YqztZic87AqutXwmzKz5VlxhSRr92YUr_T_oHd4WXmg</addsrcrecordid><sourcetype>Aggregation Database</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>77376513</pqid></control><display><type>article</type><title>Pairwise end sequencing: a unified approach to genomic mapping and sequencing</title><source>ScienceDirect Freedom Collection 2022-2024</source><creator>Roach, Jared C. ; Boysen, Cecilie ; Wang, Kai ; Hood, Leroy</creator><creatorcontrib>Roach, Jared C. ; Boysen, Cecilie ; Wang, Kai ; Hood, Leroy</creatorcontrib><description>Strategies for large-scale genomic DNA sequencing currently require physical mapping, followed by detailed mapping, and finally sequencing. The level of mapping detail determines the amount of effort, or sequence redundancy, required to finish a project. Current strategies attempt to find a balance between mapping and sequencing efforts. One such approach is to employ strategies that use sequence data to build physical maps. Such maps alleviate the need for prior mapping and reduce the final required sequence redundancy. To this end, the utility of correlating pairs of sequence data derived from both ends of subcloned templates is well recognized. However, optimal strategies employing such pairwise data have not been established. In the present work, we simulate and analyze the parameters of pairwise sequencing projects including template length, sequence read length, and total sequence redundancy. One pairwise strategy based on sequencing both ends of plasmid subclones is recommended and illustrated with raw data simulations. We find that pairwise strategies are effective with both small (cosmid) and large (megaYAC) targets and produce ordered sequence data with a high level of mapping completeness. They are ideal for fine-scale mapping and gene finding and as initial steps for either a high- or a low-redundancy sequencing effort. Such strategies are highly automatable.</description><identifier>ISSN: 0888-7543</identifier><identifier>EISSN: 1089-8646</identifier><identifier>DOI: 10.1016/0888-7543(95)80219-C</identifier><identifier>PMID: 7601461</identifier><language>eng</language><publisher>San Diego, CA: Elsevier Inc</publisher><subject>Base Composition ; Biological and medical sciences ; chromosome mapping ; Chromosome Mapping - methods ; Computer Simulation ; Cosmids - genetics ; Diverse techniques ; Fundamental and applied biological sciences. Psychology ; Genome ; Molecular and cellular biology ; sequence analysis ; Sequence Analysis, DNA - methods ; Templates, Genetic</subject><ispartof>Genomics (San Diego, Calif.), 1995-03, Vol.26 (2), p.345-353</ispartof><rights>1995</rights><rights>1995 INIST-CNRS</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c487t-dd4ce0fe3589088ec93b26f337d59edfaf0f54a654ab6411e89a215c1bba16bb3</citedby><cites>FETCH-LOGICAL-c487t-dd4ce0fe3589088ec93b26f337d59edfaf0f54a654ab6411e89a215c1bba16bb3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>315,786,790,27957,27958</link.rule.ids><backlink>$$Uhttp://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=3500863$$DView record in Pascal Francis$$Hfree_for_read</backlink><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/7601461$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Roach, Jared C.</creatorcontrib><creatorcontrib>Boysen, Cecilie</creatorcontrib><creatorcontrib>Wang, Kai</creatorcontrib><creatorcontrib>Hood, Leroy</creatorcontrib><title>Pairwise end sequencing: a unified approach to genomic mapping and sequencing</title><title>Genomics (San Diego, Calif.)</title><addtitle>Genomics</addtitle><description>Strategies for large-scale genomic DNA sequencing currently require physical mapping, followed by detailed mapping, and finally sequencing. The level of mapping detail determines the amount of effort, or sequence redundancy, required to finish a project. Current strategies attempt to find a balance between mapping and sequencing efforts. One such approach is to employ strategies that use sequence data to build physical maps. Such maps alleviate the need for prior mapping and reduce the final required sequence redundancy. To this end, the utility of correlating pairs of sequence data derived from both ends of subcloned templates is well recognized. However, optimal strategies employing such pairwise data have not been established. In the present work, we simulate and analyze the parameters of pairwise sequencing projects including template length, sequence read length, and total sequence redundancy. One pairwise strategy based on sequencing both ends of plasmid subclones is recommended and illustrated with raw data simulations. We find that pairwise strategies are effective with both small (cosmid) and large (megaYAC) targets and produce ordered sequence data with a high level of mapping completeness. They are ideal for fine-scale mapping and gene finding and as initial steps for either a high- or a low-redundancy sequencing effort. Such strategies are highly automatable.</description><subject>Base Composition</subject><subject>Biological and medical sciences</subject><subject>chromosome mapping</subject><subject>Chromosome Mapping - methods</subject><subject>Computer Simulation</subject><subject>Cosmids - genetics</subject><subject>Diverse techniques</subject><subject>Fundamental and applied biological sciences. Psychology</subject><subject>Genome</subject><subject>Molecular and cellular biology</subject><subject>sequence analysis</subject><subject>Sequence Analysis, DNA - methods</subject><subject>Templates, Genetic</subject><issn>0888-7543</issn><issn>1089-8646</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>1995</creationdate><recordtype>article</recordtype><recordid>eNp9kF1rFDEUhkOx1LX6DyrmQsRejCaTj0m8EGTRVmhRaHsdziQn25SdmW2ya_Hfm3WXBW-8CIGc55zz5iHkjLMPnHH9kRljmk5J8d6qc8Nabpv5EZlxZmxjtNTPyOyAPCcvSnlgjFlh2hNy0mnGpeYzcv0TUn5KBSmOgRZ83ODo07j4RIFuxhQTBgqrVZ7A39P1RBc4TkPydKiPFaPwT9dLchxhWfDV_j4ld9--3s4vm6sfF9_nX64aL023bkKQHllEoYytEdFb0bc6CtEFZTFEiCwqCbqeXkvO0VhoufK874Hrvhen5N1ubg1Wd5e1G1LxuFzCiNOmuK4TnVZcVFDuQJ-nUjJGt8ppgPzbcea2Ft1Wkdsqcla5vxbdvLa93s_f9AOGQ9NeW62_3deheFjGDPX75YAJxZjR2-1vdliEycEiV-TupmVcMK5YqztZic87AqutXwmzKz5VlxhSRr92YUr_T_oHd4WXmg</recordid><startdate>19950320</startdate><enddate>19950320</enddate><creator>Roach, Jared C.</creator><creator>Boysen, Cecilie</creator><creator>Wang, Kai</creator><creator>Hood, Leroy</creator><general>Elsevier Inc</general><general>Elsevier</general><scope>FBQ</scope><scope>IQODW</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope></search><sort><creationdate>19950320</creationdate><title>Pairwise end sequencing: a unified approach to genomic mapping and sequencing</title><author>Roach, Jared C. ; Boysen, Cecilie ; Wang, Kai ; Hood, Leroy</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c487t-dd4ce0fe3589088ec93b26f337d59edfaf0f54a654ab6411e89a215c1bba16bb3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>1995</creationdate><topic>Base Composition</topic><topic>Biological and medical sciences</topic><topic>chromosome mapping</topic><topic>Chromosome Mapping - methods</topic><topic>Computer Simulation</topic><topic>Cosmids - genetics</topic><topic>Diverse techniques</topic><topic>Fundamental and applied biological sciences. Psychology</topic><topic>Genome</topic><topic>Molecular and cellular biology</topic><topic>sequence analysis</topic><topic>Sequence Analysis, DNA - methods</topic><topic>Templates, Genetic</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Roach, Jared C.</creatorcontrib><creatorcontrib>Boysen, Cecilie</creatorcontrib><creatorcontrib>Wang, Kai</creatorcontrib><creatorcontrib>Hood, Leroy</creatorcontrib><collection>AGRIS</collection><collection>Pascal-Francis</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><jtitle>Genomics (San Diego, Calif.)</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Roach, Jared C.</au><au>Boysen, Cecilie</au><au>Wang, Kai</au><au>Hood, Leroy</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Pairwise end sequencing: a unified approach to genomic mapping and sequencing</atitle><jtitle>Genomics (San Diego, Calif.)</jtitle><addtitle>Genomics</addtitle><date>1995-03-20</date><risdate>1995</risdate><volume>26</volume><issue>2</issue><spage>345</spage><epage>353</epage><pages>345-353</pages><issn>0888-7543</issn><eissn>1089-8646</eissn><notes>ObjectType-Article-1</notes><notes>SourceType-Scholarly Journals-1</notes><notes>ObjectType-Feature-2</notes><notes>content type line 23</notes><abstract>Strategies for large-scale genomic DNA sequencing currently require physical mapping, followed by detailed mapping, and finally sequencing. The level of mapping detail determines the amount of effort, or sequence redundancy, required to finish a project. Current strategies attempt to find a balance between mapping and sequencing efforts. One such approach is to employ strategies that use sequence data to build physical maps. Such maps alleviate the need for prior mapping and reduce the final required sequence redundancy. To this end, the utility of correlating pairs of sequence data derived from both ends of subcloned templates is well recognized. However, optimal strategies employing such pairwise data have not been established. In the present work, we simulate and analyze the parameters of pairwise sequencing projects including template length, sequence read length, and total sequence redundancy. One pairwise strategy based on sequencing both ends of plasmid subclones is recommended and illustrated with raw data simulations. We find that pairwise strategies are effective with both small (cosmid) and large (megaYAC) targets and produce ordered sequence data with a high level of mapping completeness. They are ideal for fine-scale mapping and gene finding and as initial steps for either a high- or a low-redundancy sequencing effort. Such strategies are highly automatable.</abstract><cop>San Diego, CA</cop><pub>Elsevier Inc</pub><pmid>7601461</pmid><doi>10.1016/0888-7543(95)80219-C</doi><tpages>9</tpages></addata></record> |
fulltext | fulltext |
identifier | ISSN: 0888-7543 |
ispartof | Genomics (San Diego, Calif.), 1995-03, Vol.26 (2), p.345-353 |
issn | 0888-7543 1089-8646 |
language | eng |
recordid | cdi_proquest_miscellaneous_77376513 |
source | ScienceDirect Freedom Collection 2022-2024 |
subjects | Base Composition Biological and medical sciences chromosome mapping Chromosome Mapping - methods Computer Simulation Cosmids - genetics Diverse techniques Fundamental and applied biological sciences. Psychology Genome Molecular and cellular biology sequence analysis Sequence Analysis, DNA - methods Templates, Genetic |
title | Pairwise end sequencing: a unified approach to genomic mapping and sequencing |
url | http://sfxeu10.hosted.exlibrisgroup.com/loughborough?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2024-09-21T17%3A09%3A35IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-proquest_cross&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Pairwise%20end%20sequencing:%20a%20unified%20approach%20to%20genomic%20mapping%20and%20sequencing&rft.jtitle=Genomics%20(San%20Diego,%20Calif.)&rft.au=Roach,%20Jared%20C.&rft.date=1995-03-20&rft.volume=26&rft.issue=2&rft.spage=345&rft.epage=353&rft.pages=345-353&rft.issn=0888-7543&rft.eissn=1089-8646&rft_id=info:doi/10.1016/0888-7543(95)80219-C&rft_dat=%3Cproquest_cross%3E77376513%3C/proquest_cross%3E%3Cgrp_id%3Ecdi_FETCH-LOGICAL-c487t-dd4ce0fe3589088ec93b26f337d59edfaf0f54a654ab6411e89a215c1bba16bb3%3C/grp_id%3E%3Coa%3E%3C/oa%3E%3Curl%3E%3C/url%3E&rft_id=info:oai/&rft_pqid=77376513&rft_id=info:pmid/7601461&rfr_iscdi=true |